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Parameterizing adenosine-like drug molecule
#25163 08/23/10 11:15 PM
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Ascaris Offline OP
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Hello,

I have been following Kenno's tutorial as I attempt to parameterize a (methylthio-)adenosine-like drug molecule, BuT-DADMe-Immucillin-A. I am at the stage of selecting 'initial guess' ANGLE parameters, and have been using the mispar script that Kenno provided to suggest existing parameters that may be similar to the parameters that CHARMM reports as missing...

Unexpectedly, CHARMM requests two ANGLE parameters

Quote:

<CODES>: No angle parameters for 43 ( NG2R51 CG2RC0 CG2R64 )
<CODES>: No angle parameters for 57 ( CG2R51 CG2RC0 NG2R62 )
<CODES>: A TOTAL OF 2 MISSING PARAMETERS


when nowhere in the rtf are CG2RC0 and CG2R64 or CG2RCO and NG2R62 listed as bonded to each other. In other words, no such angle should exist to require parameters...

Now, the atoms in question are all involved in double bonds, and I'd originally listed the double bonds in the rtf using DOUBLE, after listing all the single bonds using BOND. After (re)reading about the equivalency of BOND and DOUBLE in CHARMM, I tried listing the double bonds using BOND instead of DOUBLE in the rtf; the outcome was the same.

Here is the (slightly) modified version of Kenno's generate_tutorial input script that I used:
Click to reveal..

* Structure Optimization
*

ioformat extended
prnl 7
set pdbdir .


!### Things that should be reconsidered for every molecule ###
set residue bda
set charmult 0 1
set zeed 1 C4 1 C5 1 C6 ! seed
set frist none ! first capping residue
set lsat none ! last capping residue
set small 1 !small job; use different resource usage for mp2 calculation
set bombover 0 !needs to be set to -1 for 3-membered rings

!### The variables ffsuffix and mispar were introduced ###
!### for the sake of the tutorial. ###
set ffsuffix _remas

set TOPPAR ..
open unit 10 read card name @TOPPAR/top_all36_cgenff@ffsuffix.rtf
read rtf card unit 10
close unit 10
open unit 10 read card name @TOPPAR/par_all36_cgenff@ffsuffix.prm
read para card flex unit 10
close unit 10

if @?str eq 1 stream @str
!Gaussian resource usage
if @small eq 0 then
set mem 480MW
set nproc 4
endif
if @small eq 1 then
set mem 96MW
set nproc 1
endif

read sequence card
* @residue
*
1
@residue

bomlev @bombover
generate @residue first @frist last @lsat setup warn

!generate structure from topology
if @?mispar eq 0 then
ic generate
ic param
ic seed @zeed
ic build
endif
bomlev 0
ic purge
ic print

!save initial geometry
coor print

open unit 30 write form name @residue_init.pdb
write coor pdb unit 30
close unit 30

!minimize structure and calculate dipole moment
if @dontmini eq 1 goto skip_min
MINI CONJ nstep 200 nprint 20 inbfrq 1000 cutnb 999.
MINI NRAP nstep 50 tolgrd 0.00001
prnlev 3
coor dipole oxyz select segid @residue end

!save minimized geometry
coor print
open unit 30 write form name @residue_min.crd
write coor card unit 30

open unit 30 write form name @pdbdir/@residue_min.pdb
write coor pdb unit 30
close unit 30
label skip_min

!save coordinates in comparison set
coor copy comp
ic save
ic fill
ic print

!Create gaussian file
set fname @residue
open unit 30 write form name gauss/@fname_opt_freq_mp2.gjf
prnlev 3
mmqm unit 30
%chk=@fname_opt_freq_mp2
%mem=@mem
%NProcShared=@nproc
#MP2/6-31G* NoSymm Opt=Tight pop=(mk,dipole) density=current

@residue optimized at MP2/6-31G*

@charmult
END
GAUSSIAN_BASIS


--link1--
%chk=@fname_opt_freq_mp2
%mem=@mem
%NProcShared=@nproc
#MP2/6-31G* NoSymm geom=allcheck freq IOP(7/33=1)

@residue frequency

@charmult




END
close unit 30




And I'm attaching the "toppar" file I created with initial guesses for charges and angle parameters (because the spoiler approach distorted the formatting confusingly, as seen with the skull and crossbones in the output below).

And here's the output:

Click to reveal..

1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 35b3 August 15, 2008
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.18-8.el5(x86_64)@redcat.aecom.yu.e
Created on 8/23/10 at 17:26:36 by user: matt

Maximum number of ATOMS: 25140, and RESidues: 14000
Current HEAP size: 2048000, and STACK size: 500000

Processing passed argument "str:toppar_bdad2.str"
Parameter: STR <- "TOPPAR_BDAD2.STR"
RDTITL> * STRUCTURE OPTIMIZATION
RDTITL> *

CHARMM>

CHARMM> ioformat extended
MISCOM> Expanded I/O format is used.

CHARMM> prnl 7

CHARMM> set pdbdir .
Parameter: PDBDIR <- "."

CHARMM>

CHARMM> !### Things that should be reconsidered for every molecule ###
CHARMM> set residue bda
Parameter: RESIDUE <- "BDA"

CHARMM> set charmult 0 1
Parameter: CHARMULT <- "0 1"

CHARMM> set zeed 1 C4 1 C5 1 C6 ! seed
Parameter: ZEED <- "1 C4 1 C5 1 C6"

CHARMM> set frist none ! first capping residue
Parameter: FRIST <- "NONE"

CHARMM> set lsat none ! last capping residue
Parameter: LSAT <- "NONE"

CHARMM> set small 1 !small job; use different resource usage for mp2 calculation
Parameter: SMALL <- "1"

CHARMM> set bombover 0 !needs to be set to -1 for 3-membered rings
Parameter: BOMBOVER <- "0"

CHARMM>

CHARMM> !### The variables ffsuffix and mispar were introduced ###
CHARMM> !### for the sake of the tutorial. ###
CHARMM> set ffsuffix _remas
Parameter: FFSUFFIX <- "_REMAS"

CHARMM>

CHARMM>

CHARMM>

CHARMM> set TOPPAR ..
Parameter: TOPPAR <- ".."

CHARMM> open unit 10 read card name @TOPPAR/top_all36_cgenff@ffsuffix.rtf
Parameter: TOPPAR -> ".."
Parameter: FFSUFFIX -> "_REMAS"
VOPEN> Attempting to open::../top_all36_cgenff_remas.rtf::
OPNLGU> Unit 10 opened for READONLY access to ../top_all36_cgenff_remas.rtf

CHARMM> read rtf card unit 10
MAINIO> Residue topology file being read from unit 10.
TITLE> * -------------------------------------------------------------------------- *
TITLE> * CGENFF: TOPOLOGY FOR THE CHARMM GENERAL FORCE FIELD V. 2A5 *
TITLE> * FOR SMALL MOLECULE DRUG DESIGN *
TITLE> * -------------------------------------------------------------------------- *
TITLE> * - AS MORE FUNCTIONAL GROUPS WILL BE INTRODUCED, SMALL CHANGES IN *
TITLE> * EXISTING PARAMETERS AND/OR CHARGES MAY OCCUR. *
TITLE> * - COMMENTS IN THIS FILE MAY BE MISLEADING. *
TITLE> * -------------------------------------------------------------------------- *
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG *
TITLE> * PARAMETER SET DISCUSSION FORUM *
TITLE> * -------------------------------------------------------------------------- *
TITLE> *

CHARMM> close unit 10
VCLOSE: Closing unit 10 with status "KEEP"

CHARMM> open unit 10 read card name @TOPPAR/par_all36_cgenff@ffsuffix.prm
Parameter: TOPPAR -> ".."
Parameter: FFSUFFIX -> "_REMAS"
VOPEN> Attempting to open::../par_all36_cgenff_remas.prm::
OPNLGU> Unit 10 opened for READONLY access to ../par_all36_cgenff_remas.prm

CHARMM> read para card flex unit 10

PARAMETER FILE BEING READ FROM UNIT 10
TITLE> * -------------------------------------------------------------------------- *
TITLE> * CGENFF: PARAMETERS FOR THE CHARMM GENERAL FORCE FIELD V. 2A5 *
TITLE> * FOR SMALL MOLECULE DRUG DESIGN *
TITLE> * -------------------------------------------------------------------------- *
TITLE> * - AS MORE FUNCTIONAL GROUPS WILL BE INTRODUCED, SMALL CHANGES IN *
TITLE> * EXISTING PARAMETERS AND/OR CHARGES MAY OCCUR. *
TITLE> * - COMMENTS IN THIS FILE MAY BE MISLEADING. *
TITLE> * -------------------------------------------------------------------------- *
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG *
TITLE> * PARAMETER SET DISCUSSION FORUM *
TITLE> * -------------------------------------------------------------------------- *
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM> close unit 10
VCLOSE: Closing unit 10 with status "KEEP"

CHARMM>

CHARMM> if @?str eq 1 stream @str
Parameter: STR -> "TOPPAR_BDAD2.STR"
Comparing "1" and "1".
IF test evaluated as true. Performing command
VOPEN> Attempting to open::toppar_bdad2.str::
OPNLGU> Unit 99 opened for READONLY access to toppar_bdad2.str

INPUT STREAM SWITCHING TO UNIT 99
RDTITL> * STREAM FILE WITH COMPOUND TO BE PARAMETERIZED.
RDTITL> * STEP 1: TOPOLOGY ONLY.
RDTITL> *
Parameter: IN1 <- "" <empty>

CHARMM>

CHARMM> read rtf card append
MAINIO> Residue topology file being read from unit 99.
RDTITL> * TOPOLOGY OF COMPOUND TO BE PARAMETERIZED.
RDTITL> *
WARNING FROM DECODF - COULD NOT CONVERT STRING
I
ZERO WILL BE RETURNED.
**** Warning **** The following extraneous characters
were found while command processing in RTF reader
1.00
**** WARNING from RTFRDR **** The total charge of the residue, BDA , 1.0000000,
does not equal the expected charge, 0.0000000.
There were 1 warning(s) from RTFRDR.

CHARMM>

CHARMM> read param card flex append

PARAMETER FILE BEING READ FROM UNIT 99
RDTITL> * PARAMETERS NEEDED FOR NEW MOLECULES
RDTITL> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM>

VCLOSE: Closing unit 99 with status "KEEP"

RETURNING TO INPUT STREAM 5

CHARMM>

CHARMM> !Gaussian resource usage
CHARMM> if @small eq 0 then
Parameter: SMALL -> "1"
Comparing "1" and "0".
IF test evaluated as false. Skip to ELSE or ENDIF

CHARMM> if @small eq 1 then
Parameter: SMALL -> "1"
Comparing "1" and "1".
IF test evaluated as true. Performing command

CHARMM> set mem 96MW
Parameter: MEM <- "96MW"

CHARMM> set nproc 1
Parameter: NPROC <- "1"

CHARMM> endif

CHARMM>

CHARMM> read sequence card
MAINIO> Sequence information being read from unit 5.
RDTITL> * BDA
RDTITL> *

SEQRDR> 1

SEQRDR> @residue
Parameter: RESIDUE -> "BDA"

RESIDUE SEQUENCE -- 1 RESIDUES
BDA

CHARMM>

CHARMM> bomlev @bombover
Parameter: BOMBOVER -> "0"

CHARMM> generate @residue first @frist last @lsat setup warn
Parameter: RESIDUE -> "BDA"
Parameter: FRIST -> "NONE"
Parameter: LSAT -> "NONE"
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
<CODES>: No angle parameters for 43 ( NG2R51 CG2RC0 CG2R64 )
<CODES>: No angle parameters for 57 ( CG2R51 CG2RC0 NG2R62 )
<CODES>: A TOTAL OF 2 MISSING PARAMETERS

***** LEVEL -1 WARNING FROM <CODES> *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5



/---------\
/ \
/ \
/ \
! XXXX XXXX !
! XXXX XXXX !
! XXX XXX !
! X !
--\ XXX /--
! ! XXX ! !
! ! ! !
! I I I I I !
! I I I I !
\ /
-- --
\---/
XXX XXX
XXXX XXXX
XXXXX XXXXX
XXX XXX
XXX XXX
XXXXX
XXX XXX
XXX XXX
XXX XXX
XXXXX XXXXX
XXXX XXXX
XXX XXX


Execution terminated due to the detection of a fatal error.

ABNORMAL TERMINATION
MAXIMUM STACK SPACE USED IS 21034
STACK CURRENTLY IN USE IS 50
MOST SEVERE WARNING WAS AT LEVEL -1
HEAP PRINTOUT- HEAP SIZE 2048000
SPACE CURRENTLY IN USE IS 892
MAXIMUM SPACE USED IS 892
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 2047108 NEXT: 0

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 2.21 SECONDS
CPU TIME: 2.21 SECONDS




I have checked the formatting of the rtf against rtop.doc, and I have double-checked that all the bonds, and no others, are listed in the rtf. Any ideas what I might be doing wrong?



Also, I do have another question for Kenno specifically about the tutorial. You write:
Quote:
(the IC table is not required for energy calculations if Cartesian coordinates for the molecule are present) ... Creation of the BOND list and the IC table (which may be performed via the IC GENErate command) will not be discussed further.

Do you write that this will not be discussed further because it is covered at length somewhere else? As you can see, I do not have any ICs listed, which may (or may not) be a problem (but I don't think this is causing the extraneous ANGLE parameter request discussed above)...

Many thanks,

-A.L.



Attached Files
toppar_bdad2_str.txt (4.26 KB, 367 downloads)
initial "toppar" for BuT-MeDAD-Immucillin-A
Last edited by Ascaris; 08/23/10 11:16 PM.
Re: Parameterizing adenosine-like drug molecule
Ascaris #25165 08/24/10 06:51 AM
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How about N3-C4-C9 and N7-C5-C6?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Parameterizing adenosine-like drug molecule
lennart #25171 08/24/10 06:42 PM
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Ascaris Offline OP
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Wow. Sometimes you can't see what's staring you right in the face. [sheepish grin] Evidently, I was overlooking the fact that more than one atom in the rings have the same atom type (NG2R62 and CG2R64) when I was looking at the missing parameters. Brilliant.

Thanks very much for your help and apologies for not catching that.


Intestinal nematode
Bronx, NY
Re: Parameterizing adenosine-like drug molecule
Ascaris #25194 08/27/10 04:03 AM
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Originally Posted By: Ascaris
You write:
Quote:
(the IC table is not required for energy calculations if Cartesian coordinates for the molecule are present) ... Creation of the BOND list and the IC table (which may be performed via the IC GENErate command) will not be discussed further.
Do you write that this will not be discussed further because it is covered at length somewhere else?
  • The BOND list is not discussed further because it's absolutely trivial. You don't even need to use the keywords DOUBLE and TRIPLE; all bonds are BOND.
  • The IC table format is described in the CHARMM documentation (as is the BOND list), and it's not strictly needed if you manage to construct a file with cartesian coordinates that CHARMM will accept.(*) I'm thinking about giving the tutorial a little update in a few months, and if I do, it will contain example scripts on how to generate a molecule without an IC table.


(*)Warning! CHARMM is ridiculously picky in this respect and you may end up banging your head against your keyboard. We are not responsible for any physical or mental injuries or material damage caused by using CHARMM.

Re: Parameterizing adenosine-like drug molecule
Kenno #25198 08/27/10 04:59 AM
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It should be noted that, possibly except for chiral centers, it is not necessary to specify IC entries for any H atoms; HBUILD does a very good job, and does not need IC table entries. I've found that hand made IC tables, with only the dihedrals specified, make a good starting point for model building. Setting the bond and angle values (positions 1, 2, 4, and 5) to 0.00 allows those values to be assigned from the parameters via IC PARAM.


Rick Venable
computational chemist

Re: Parameterizing adenosine-like drug molecule
Kenno #25300 09/02/10 07:42 PM
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Ascaris Offline OP
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Quote:
The BOND list is not discussed further because it's absolutely trivial. You don't even need to use the keywords DOUBLE and TRIPLE; all bonds are BOND.
Kenno, I agree that the bond list is trivial; I should have used an ellipsis in place of "BOND list." But I do find the documentation about the IC sections of an rtf rather unenlightening in terms of creating an rtf...

Which is why your suggestion is much appreciated, Rick. Putting that immediately to use, I came up with the attached stream file, for the adenine-like fragment of my drug molecule. [Please see attached.]

Does this look reasonable? Are the IC dihedrals over- or under-defined?

The assignment of (non-improper) dihedrals seemed straightforward, but I did notice that some improper dihedrals for existing residues (such as adenosine) sometimes assigned improper dihedrals of -180. I believe I read somewhere that this is a function of the order of the atoms listed but I could not envision a situation in which an assignment of 180 for the impropers would be inappropriate, so that is what I used for all of the impropers in this planar fragment...

I used output of the adapted generate_tutorial.inp script to determine the missing parameters and mispar to help find analogous ones, which I "renamed" and added to the parameter section of the toppar stream file as seen.

However, when I tried to run the script at this point, the first thing I noticed is that a value of 1 for the variable mispar is generated and the script skips the ic generate, ic param, ic seed (zeed), and ic build. I tried setting the variable value to 0 to no avail (not sure why this was unsuccessful). [See attached output file ...16.out]

Then, I simply removed the conditional so that the script necessarily went through the ic generate, ic param, etc. commands. [see attached file generate_fragment1b.inp] However, at the point of
ic param
CHARMM crashes with the following error:
***** LEVEL -1 WARNING FROM <CODES> *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

But which parameters might be needed is not specified. [See attached output file ...1b_6.out] Can someone help explain to me what's going on?

Many thanks,

al

Attached Files
toppar_frg1_3_str.txt (3.89 KB, 383 downloads)
generate_fragment1b_inp.txt (2.46 KB, 454 downloads)
generate_frg1b_6_out.txt (10.53 KB, 380 downloads)
generate_frg1_16_out.txt (58.97 KB, 384 downloads)

Intestinal nematode
Bronx, NY
Re: Parameterizing adenosine-like drug molecule
Ascaris #25303 09/02/10 09:34 PM
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So, I lowered to bomb level to see if I could get some more info on what's going on, and here's what the output is (the whole file is attached):
Quote:

CHARMM> ic param

***** LEVEL -1 WARNING FROM <CODES> *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

%BUILDC-WARNING: no angle parameters for types (NG2R62 ,CG2RC0 ,CG2R64 )

So heaven help me if I'm not able to see the angle this time, but I really can't see how this allegedly missing parameter could be for an angle that's supposed to exist in my molecule. These atom types correspond to N1/N3, C4/C5, and C1/C6. All are connected, but not in that order (unless I'm being totally blind here--I've checked about 8 times, so for my own sake I hope not).

The output continues.
Quote:

CHARMM> ic seed @zeed
Parameter: ZEED -> "1 C4 1 C5 1 C6"

CHARMM> ic build

***** LEVEL 1 WARNING FROM <BUILDC> *****
***** SOME COORDINATES NOT BUILT
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

**** WARNING **** 5 COORDINATES ARE STILL UNDEFINED


Looking further down at the output, when the minimization begins it's clear that 5 atoms indeed have undefined coordinates (9999.0).
Quote:
CHARMM> !save initial geometry
CHARMM> coor print

COORDINATE FILE MODULE
TITLE> * STRUCTURE OPTIMIZATION
TITLE> *
16 EXT
1 1 FG1 C9 9999.0000000000 9999.0000000000 9999.
0000000000 FG1 1 0.0000000000
2 1 FG1 C5 1.3850000000 0.0000000000 0.
0000000000 FG1 1 0.0000000000
3 1 FG1 N7 1.7570756132 -1.3237011513 0.
0000000000 FG1 1 0.0000000000
4 1 FG1 C8 0.6364003461 -2.1289880230 0.
0000000000 FG1 1 0.0000000000
5 1 FG1 H8 9999.0000000000 9999.0000000000 9999.
0000000000 FG1 1 0.0000000000
6 1 FG1 N1 3.4047954266 0.9240806217 0.
0000000000 FG1 1 0.0000000000
7 1 FG1 C2 3.8083426096 -0.3558075262 0.
0000000000 FG1 1 0.0000000000
8 1 FG1 H2 9999.0000000000 9999.0000000000 9999.
0000000000 FG1 1 0.0000000000
9 1 FG1 N3 9999.0000000000 9999.0000000000 9999.
0000000000 FG1 1 0.0000000000
10 1 FG1 C4 0.0000000000 0.0000000000 0.
0000000000 FG1 1 0.0000000000
11 1 FG1 C6 2.0844217057 1.1640331944 0.
0000000000 FG1 1 0.0000000000
12 1 FG1 N6 1.3931795839 2.3422268665 0.
0000000000 FG1 1 0.0000000000
13 1 FG1 H61 1.8641914652 3.2243537325 0.
0000000000 FG1 1 0.0000000000
14 1 FG1 H62 1.8641914652 3.2243537325 0.
0000000000 FG1 1 0.0000000000
15 1 FG1 H7 2.7131913659 -1.6491895035 0.
0000000000 FG1 1 0.0000000000
16 1 FG1 H9 9999.0000000000 9999.0000000000 9999.
0000000000 FG1 1 0.0000000000

Those atoms are C9, H8, H2, N3, and H9. Not sure why these particular atoms are missing, but I assume it has something to do with an error I made when creating the topology file for this "residue". Which I think takes me back to my previous post and my question about how the toppar[].str file looks...

Attached Files
generate_frg1b_8_out.txt (18.96 KB, 384 downloads)

Intestinal nematode
Bronx, NY
Re: Parameterizing adenosine-like drug molecule
Ascaris #25308 09/02/10 09:50 PM
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The IC table may be suspect, since IC PARAM gives an error. How did you obtain the IC table itself? What you made you decide to include so many improper dihedrals?

At the risk of my repeating myself, I do not recommend using IC GENERATE for this purpose.


Rick Venable
computational chemist

Re: Parameterizing adenosine-like drug molecule
rmv #25310 09/02/10 10:42 PM
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Ah, yes, I believe I did use ic generate to create this IC table (because of what Kenno said in his tutorial about being able to use that command to generate an IC table). When you say at risk of repeating yourself, are you referring to a thread (entitled, "Confused about generating dihedral basis set") in which you recommended using "GENErate SETUp" instead of ic gene? Or a different thread that I'm missing? ... What should I use to "obtain" my IC table? confused

I defined so many impropers in the IC table because of my use of IC generate, and I think I may have added one or two after looking at the rtf for an adenine-containing molecule... If one is not using IC gene, how does one determine what dihedrals (proper and improper) need to be listed in the IC table of the rtf? The output of GENE SETU? In fact, I'm not even sure how many lines my rtf's IC table should contain... but that takes me back to my question in the previous paragraph.


Intestinal nematode
Bronx, NY
Re: Parameterizing adenosine-like drug molecule
Ascaris #25311 09/02/10 10:56 PM
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I recommend making the IC table by hand; to quote intcor.doc--

The main purpose for this command is to be able to easily produce an
IC table for internal coordinate analysis. The simple algorithm employed
here does not do a very good job of guessing reasonable IC dihedral values
for use in coordinate building such as;
IC GENErate ...
IC PARAM
IC SEED ...
IC BUILD

Ring systems are also cited as being problematic for IC GENERATE.

The SETUP option of GENERATE uses whatever IC entries are listed in the RESIdue definition.


Rick Venable
computational chemist

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