CHARMM Development Project
Posted By: Hem@1 parameters for BOC group - 01/02/17 11:02 AM
Is the parameter for Boc group available.
Posted By: rmv Re: parameters for BOC group - 01/02/17 05:12 PM
Yes and no. The atom types and bonded terms are likely available, but there may not be an existing residue topology in the distributed files.

A couple quick searches with grep did not find BOC alone, but there are some complex molecules with the fragment in top_all36_cgenff.rtf which could probably be used as a basis to create a patch (PRES) for replacing an amino group.
Posted By: lennart Re: parameters for BOC group - 01/02/17 06:11 PM
So paramchem.org might work?
Posted By: rmv Re: parameters for BOC group - 01/02/17 06:23 PM
Probably, but I'd use existing fragments from the CGenFF topology file (search for Tert.Butyl) if I needed this for my work. The CGenFF guidelines advise using existing topologies when available, instead of those from cgenff program or its web interface, ParamChem.
Posted By: alex Re: parameters for BOC group - 01/16/17 10:44 PM
Paramchem would work pretty well with BOC. The penalties should be rather small.
Posted By: Hem@1 Re: parameters for BOC group - 01/19/17 11:57 AM
Ya,
I have the received the parameter file from CGenFF paramchem in .str format.

the group is defined as "RESI/ scrat". this I have written it as PRES BOC.

(since the atom name C (CG202) should bind with +N of Resi Trp)

in the bond defination i have replaced H02 atom with +N (which earlier binds with C) and following an earlier example i have scripted the setup file as

read sequ card
* peptide seq
*
5
trp thr val ser ala

gener pep setup warn first boc last ct3



the warning in the output as

PARAMETER FILE BEING READ FROM UNIT 99
RDTITL> * PARAMETERS GENERATED BY ANALOGY BY
RDTITL> * CHARMM GENERAL FORCE FIELD (CGENFF) PROGRAM VERSION 1.0.0
RDTITL> *
PARRDR> WARNING: ATOMS IN BOND CG2O OG2D 750.00000 1.22000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG2O OG30 150.00000 1.33400 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG2O N 260.00000 1.30000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG30 CG33 222.50000 1.53800 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG30 OG30 340.00000 1.43000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CG33 HGA3 322.00000 1.11100 DONT EXIST
PARRDR> WARNING: ATOMS IN ANGLE OG2D CG2O OG30 90.00000 125.90000 DONT EXIST
**** Warning **** The following extraneous characters
were found while command processing in PARRDR
160.00 2.25760


How should I do the Patch?
Posted By: Hem@1 Re: parameters for BOC group - 01/19/17 12:02 PM
Hello,

In the above post I have given various detatils of the input and output (enough to make RMV and lennart red with anger).

my point is how should i patch the BOC group with my the N terminal of the first residue (in my case it is TRP)
Posted By: Hem@1 Re: parameters for BOC group - 01/19/17 12:04 PM
* Toppar stream file generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
* For use with CGenFF version 3.0.1
*

read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*
36 1

! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

RESI /scrat 0.000 ! param penalty= 108.000 ; charge penalty= 8.368
GROUP ! CHARGE CH_PENALTY
ATOM C CG2O2 0.557 ! 7.505
ATOM C1 CG331 -0.270 ! 0.622
ATOM O1 OG2D1 -0.456 ! 0.525
ATOM C2 CG331 -0.270 ! 0.622
ATOM O2 OG302 -0.445 ! 8.368
ATOM C3 CG331 -0.270 ! 0.622
ATOM CT CG301 0.232 ! 4.616
ATOM H01 HGA3 0.090 ! 0.025
ATOM H02 HGR52 0.112 ! 2.610
ATOM H03 HGA3 0.090 ! 0.025
ATOM H04 HGA3 0.090 ! 0.025
ATOM H05 HGA3 0.090 ! 0.025
ATOM H06 HGA3 0.090 ! 0.025
ATOM H07 HGA3 0.090 ! 0.025
ATOM H08 HGA3 0.090 ! 0.025
ATOM H09 HGA3 0.090 ! 0.025
ATOM H10 HGA3 0.090 ! 0.025

BOND C O1
BOND C O2
BOND C H02
BOND C1 CT
BOND C1 H03
BOND C1 H06
BOND C1 H09
BOND C2 CT
BOND C2 H04
BOND C2 H07
BOND C2 H10
BOND O2 CT
BOND C3 CT
BOND C3 H01
BOND C3 H05
BOND C3 H08
IMPR C O1 O2 H02

END

read param card flex append
* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 1.0.0
*

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

BONDS
CG2O2 OG2D1 750.00 1.2200 ! PROT adm jr. 5/02/91, acetic acid pure solvent; LIPID methyl acetate
CG2O2 OG302 150.00 1.3340 ! LIPID methyl acetate
CG2O2 HGR52 348.00 1.0960 ! FORH, formic acid, xxwy
CG301 CG331 222.50 1.5380 ! RETINOL TMCH/MECH
CG301 OG302 340.00 1.4300 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide
CG331 HGA3 322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92

ANGLES
OG2D1 CG2O2 OG302 90.00 125.90 160.00 2.25760 ! LIPID acetic acid
OG2D1 CG2O2 HGR52 39.00 119.00 ! FORH, formic acid, xxwy
OG302 CG2O2 HGR52 47.00 105.00 ! /scrat , from OG311 CG2O2 HGR52, PENALTY= 15
CG331 CG301 CG331 58.35 113.50 11.16 2.56100 ! RETINOL TMCH/MECH
CG331 CG301 OG302 75.70 110.10 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha
CG301 CG331 HGA3 33.43 110.10 22.53 2.17900 ! RETINOL TMCH/MECH
HGA3 CG331 HGA3 35.50 108.40 5.40 1.80200 ! PROT alkane update, adm jr., 3/2/92
CG2O2 OG302 CG301 40.00 109.60 30.00 2.26510 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha

DIHEDRALS
OG2D1 CG2O2 OG302 CG301 0.9650 1 180.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide !cacha,corrected kevo, 01/08
OG2D1 CG2O2 OG302 CG301 3.8500 2 180.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide !cacha,corrected kevo, 01/08
HGR52 CG2O2 OG302 CG301 2.0500 2 180.00 ! /scrat , from CG321 CG2O2 OG302 CG301, PENALTY= 108
CG331 CG301 CG331 HGA3 0.1600 3 0.00 ! RETINOL TMCH
OG302 CG301 CG331 HGA3 0.1600 3 0.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha reset to default by kevo
CG331 CG301 OG302 CG2O2 0.0000 3 0.00 ! AMGT, Alpha Methyl Gamma Tert Butyl Glu Acid CDCA Amide, cacha

IMPROPERS
CG2O2 OG2D1 OG302 HGR52 75.0000 0 0.00 ! /scrat , from CG2O2 OG2D1 OG311 HGR52, PENALTY= 1

END
RETURN
Posted By: rmv Re: parameters for BOC group - 01/19/17 06:10 PM
Study the existing patch residues, esp. N-terminal patches.

We do appreciate the people who take the time to attach longer listings as .txt files via the Full Reply Screen.

Posted By: Hem@1 Re: parameters for BOC group - 01/21/17 07:18 AM
Hello,

please find the files attached herewith.
file no 2 is named as boc.str
top_all36 and par_all36 are used.

please point me the needful to manage the patch of boc.
the output messages warns me of the missing co-ordinates

Attached File
boc.txt  (258 downloads)
Attached File
boc2.txt  (278 downloads)
Attached File
setup.txt  (304 downloads)
Posted By: rmv Re: parameters for BOC group - 01/21/17 04:29 PM
Do not use BOMLEV -5 ever, for anything; it's a waste of everyone's time to try to diagnose problems with scripts using this setting.

Try again with the default BOMLEV and address the reported errors and/or warnings.
Posted By: Hem@1 Re: parameters for BOC group - 01/23/17 03:27 PM
Hello Sir,
ya three cases :

case3: while using cgenff parameter files
+++++++++++++++++++++++++++++++++++++++++++++++++++++
CHARMM> GENERATE A setup warn first boc last CT1
***** ERROR in GENIC ***** Residue 'TRP ' was not found.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

should I use all36_prot.parameter and topology files or par_all22_prot files

earlier:




with a BOMlev 0

Leaving aside the problem of BOC patching to the first residue of my tri-mer I have gone through your "complex PDB input examples" post from script archrive.


case 1:

Now when I use the

************************************************************************
! build missing part
!-------------------
ic param
ic purge
ic fill preserve
ic build
define test sele ( .not. type H*) .and. ( .not. init) show end

! REBUILD ALL H ATOM COORDS
coor init sele type H* end
hbuild sele type H* end
define test sele .not. init show end
******************************************************************

An abnormal termination results stating
*****************************************************************
WARNING FROM HBUILD:
Attempt to construct a hydrogen bonded to the atom A 1 TRP N with unknown coordinates.
*** LEVEL 0 WARNING *** BOMLEV IS 0
BOMLEV HAS BEEN SATISFIED. TERMINATING.
*****************************************************************
while BOMLev to 1
program is terminated normally but all co-ordinates are 9999.000
******************************************************************
ATOM 1 N TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 2 HN TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 3 CA TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 4 HA TRP 1 9999.0009999.0009999.000 1.00 0.00 A
*************************************************************************



USING
***************************************************
! Chain A
!----------
open unit 3 read form name "../wwl.pdb"
read sequ pdb unit 3
close unit 3
GENERATE A setup warn first none last none
open read card unit 3 name "../wwl.pdb"
read coor pdb unit 3 resid

! build missing part
!-------------------
ic param
ic build
! build hydrogens;
!------------------------------------------
hbuild select type h* end
COOR ORIENT
!==================================================================
case 2:
the termination is normal with warnings

CHARMM> GENERATE A setup warn first none last none
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 TRP .
ATOMS "N " "-C " "CA " "HN " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 TRP .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 3 LEU .
ATOMS "C " "+N " WERE REQUESTED.
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 3 LEU .
ATOMS "C " "CA " "+N " "O " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 3 LEU .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.


AND

CHARMM> ic build
**** WARNING **** 1 COORDINATES ARE STILL UNDEFINED
****************************************************************************
Posted By: rmv Re: parameters for BOC group - 01/23/17 08:43 PM
The standard topology and parameter files include amino acids, nucleic acids, sugars, lipids, and ethers. CGenFF is only for special molecules not found in the standard CHARMM RTF and PARAM files. CHARMM parameter sets are updated ca. annually, so you should use the "all36_prot" RTF/PARAM file pair from the same point distribution as the "all36_cgenff" files.

The HBUILD error and IC BUILD warning indicate the IC table may not be set up properly. The IC entries in the PRES may not be sufficient to couple the two fragments; I didn't see any out of residue declarations (see rtop.doc, io.doc). Note that IC entries are only essential for heavy atoms; terms for H atoms can be added later, if needed (e.g. for a chiral center).
Posted By: Hem@1 Re: parameters for BOC group - 01/25/17 10:34 AM
Sorry to ask you repeatedly; for patching the BOC molecule to TRP residue i had to add "cgenff" rtf/prm files.

But whenever i add "cgenff" rtf/prm files alongwith the "all36_prot" rtf/prm files (irrespective of patching the BOC molecule or not) i get an error message stating ***** ERROR in GENIC ***** Residue 'TRP ' was not found.

else without the 'cgenff' files the program executes normally for the protein. (with all36_prot rtf/prm)
Posted By: rmv Re: parameters for BOC group - 01/25/17 07:05 PM
When reading multiple RTF/PARAM file pairs, all but the first pair must use the APPEND option, or any previous data read is discarded.

Also, all of the PARAM files must use the FLEX option.
Posted By: Hem@1 Re: parameters for BOC group - 01/27/17 12:09 PM
Thank you Sir for your advice
,
i have warnings
SPATIAL COORDINATES BEING READ FROM UNIT 3
TITLE> *
** WARNING ** After reading, there are no coordinates for selected atom: 2 1 TRP HN
** WARNING ** After reading, there are no coordinates for selected atom: 4 1 TRP HA
** WARNING ** After reading, there are no coordinates for selected atom: 6 1 TRP HB1

and in the pdb file the co-ordinates of atoms of BOC molecule are replaced by
ATOM 25 CP TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 26 C1 TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 27 O1 TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 28 C2 TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 29 O2 TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 30 C3 TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 31 CT TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 32 H01 TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 33 H03 TRP 1 9999.0009999.0009999.000 1.00 0.00 A
ATOM 34 H04 TRP 1 9999.0009999.0009999.000 1.00 0.00 A


Need further suggestion

Attached File
par_all36_cgenff.txt  (485 downloads)
Attached File
setup_inp.txt  (247 downloads)
Attached File
setup_pdb.txt  (241 downloads)
Attached File
top_all36_cgenff.txt  (344 downloads)
Attached File
setup_out.txt  (317 downloads)
Posted By: rmv Re: parameters for BOC group - 01/27/17 04:38 PM
One issue may be that the PATCH commands in setup_out.txt do not include the SETUP keyword, so any IC entries will be ignored. However, I think it may be best to revert to

GENERATE A setup warn first boc last CT1

as you have in setup_inp.txt; the posted files are not consistent.

For BOC, you have not defined any IC entries, so coordinates cannot be built.

Modifying the distributed files is highly discouraged; your added topology and parameter definitions should be in a separate stream file, in the same style as those found in toppar/stream subdirectories.
Posted By: Hem@1 Re: parameters for BOC group - 02/15/17 10:00 AM
i have tried the 'boc' molecule to patch with TRP residue both as a stream file and by attaching the content to top/par all36_cgenff (though not encouraged).
I have also incorporated the IC table as produced by the paratool of NAMD2.

how ever the error remains the same of missing 17 co-ordinates (and that too of the pathched residue)

please point me my mistake.

Attached File
setup_input.txt  (235 downloads)
Attached File
stream_boc.txt  (229 downloads)
Attached File
top_all36_cgenff.txt  (288 downloads)
Attached File
par_all36_cgenff.txt  (240 downloads)
Posted By: rmv Re: parameters for BOC group - 02/15/17 04:33 PM
There is no reason to be adding ANGL and DIHE entries to topology files any longer (see rtop.doc); that makes the BOC patch highly problematic. The correct procedure is to use AUTOGENERATE to define those terms, based on the bonded topology.

For IC entries, forget about H atoms for now, and focus exclusively on the heavy atoms; HBUILD can place H atoms w/o the need for IC entries. In particular, it is wise to avoid having the same two atoms in the second and third position in more than one IC entry.

Your mistake may be using NAMD.

Keep posted attachments smaller if you want people to actually look at them; consider posting just your changes to large files such as the CGenFF RTF and PARAM files.

Posted By: lennart Re: parameters for BOC group - 02/15/17 04:50 PM
And please do not set BOMLEV -5.
Posted By: rmv Re: parameters for BOC group - 02/15/17 05:56 PM
Especially when you've already been warned about that.
© CHARMM forums