Previous Thread
Next Thread
Print Thread
Page 1 of 2 1 2
biotin parameters
#22637 10/28/09 01:02 PM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
Hi everybody,
I'm trying to build a biotinilated peptide, i found some biotin parameterization but when I tried to build the peptide i found some problems and i think that my problems are related to the parameters. Do you have some advices about it?
thank you in advance

Attached Files
biotOut.txt (6.85 KB, 428 downloads)
biotb4.txt (1014 Bytes, 396 downloads)
Re: biotin parameters
FranciT #22638 10/28/09 01:28 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
You have randomly changed the order of commands
IC PARA
IC SEED
IC BUIL
HBUILD
What you have will not work.

You want to use CHARMM formatted coordinate files rather than PDB as far as possible (PDB is an export/import format).
The PSF does not change when you minimize, so no need to save it all the time.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22643 10/28/09 02:49 PM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
thank you very much for your help,
but when I tried to build this structure, this is the error related to parameters, how can I do?
thank you in advance

<CODES>: No bond parameters for 26 ( CN1 ON1 )
<CODES>: No torsion parameters for 47 ( CP1 NN2U CN1 ON1 )
<CODES>: No torsion parameters for 48 ( CP1 NN2U CN1 NN2U)
<CODES>: No torsion parameters for 53 ( CP1 NN2U CN1 ON1 )
<CODES>: No torsion parameters for 54 ( CP1 NN2U CN1 NN2U)
<CODES>: No torsion parameters for 62 ( ON1 CN1 NN2U HN2 )
<CODES>: No torsion parameters for 63 ( ON1 CN1 NN2U HN2 )
<CODES>: No torsion parameters for 69 ( NN2U CN1 NN2U HN2 )
<CODES>: No torsion parameters for 73 ( NN2U CN1 NN2U HN2 )
<CODES>: A TOTAL OF 9 MISSING PARAMETERS

Re: biotin parameters
FranciT #22657 10/28/09 09:20 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
It seems that the RTF and PARAmeter files you have are incomplete wrt biotin (or possibly not used in the correct way); you could check with the person/group that provided the files.
Or you add the missing parameters to the parameter file - this could be straightforward if parameters for similar groups are already available.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22688 11/02/09 11:42 AM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
thank you for your help. Unfortunately i don't understand what happens to my input file because it doesn't work. Can you help me?

i attached all the file in use input/output
and the params.
thank you very much in advance

Attached Files
b3.txt (684 Bytes, 354 downloads)
b3Out.txt (7.64 KB, 609 downloads)
parBna.txt (241.16 KB, 414 downloads)
topBna.txt (108.04 KB, 520 downloads)
Re: biotin parameters
FranciT #22689 11/02/09 12:36 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
Remove the BOMLEV -2 command.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22690 11/02/09 02:42 PM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
in this way I had the error

BTN GLY GLY GLY THR

***** LEVEL 0 WARNING FROM <CHARMM> *****
***** Unrecognized command: BTN
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

but in the top and param file I added the BTN group, so I don't know why it doesn't recognize BTN.
thank you in advance

Re: biotin parameters
FranciT #22691 11/02/09 05:04 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
Because BTN is not a CHARMM command, which is exactly what the error message tells you.

I think you need something like this:
read sequence card
* peptide part
*
4
GLY GLY GLY THR
gene pept setup ! possibly with FIRST/LAST specifications

read sequence btn 1
gene btn setup

In addition you will need to create the bond between biotin and the peptide, possiblby using a PATCh command which requires the appropriate PRES to be present in your RTF.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22694 11/03/09 09:40 AM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
thank you so much i'll try to build the peptide using your precious advices.
Thank you again

Re: biotin parameters
lennart #22695 11/03/09 11:18 AM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
Here I am again,
sorry if I look like too intrusive,
so I follow your advice Prof. Lennart, and I generated a pdb, unfortunately the coordinates for the btn residue still non defined and i don't understand why
to link the two segments i modified PRES LINk (as it possible to see down here. (i used this patch because the link that the biotin form with the residue is similar to a peptidic link, i've just changed the name of the atoms)
thank you again




PRES LINK 0.00 ! linkage for IMAGES or for joining segments
! 1 refers to previous (N terminal)
! 2 refers to next (C terminal)
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
BOND 1C1 2N
IMPR 2N 1C1 2CA 2HN 1C1 1C10 2N 1O1
IC 1O1 1C10 1C1 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1C10 *1C1 1O1 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C10 1C1 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C1 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C1 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000

Attached Files
b3inp.txt (661 Bytes, 383 downloads)
b3Out.txt (8.97 KB, 369 downloads)
b3.pdb (5.32 KB, 292 downloads)
Re: biotin parameters
FranciT #22696 11/03/09 11:38 AM
Joined: Sep 2003
Posts: 4,796
Likes: 2
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
There is no structural information (no IC table) in your RESI BTN. Best is if you have a real structure (PDB file) for biotin. You can try to add the commnand IC GENERATE before IC PARAM (see intcor.doc); note that this is a poor substitute for a carefully constructed IC table.

You need to "follow [the PATCh commnad ]with AUTOgenerate ANGLes DIHEdrals command".
You probably do not want LAST NONE for your peptide.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22697 11/03/09 02:29 PM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
i have the pdb file for biotin
but when i run the input file
it gave me this error

charmm <b3.inp> b3out.txt
fmt: read unexpected character
apparent state: unit 27 named BTN.PSF
last format: (I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8,2G14.6)
lately reading sequential formatted external IO
Abort trap

Attached Files
btn.pdb (2.58 KB, 333 downloads)
Re: biotin parameters
FranciT #22698 11/03/09 02:53 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
So there was an unexpected character in your file. Difficult to diagnose without any information.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22699 11/03/09 03:16 PM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
these are my files
thank you again

Attached Files
btn.pdb (2.58 KB, 437 downloads)
btn.psf (8.13 KB, 323 downloads)
b3inp.txt (832 Bytes, 350 downloads)
Re: biotin parameters
FranciT #22700 11/03/09 03:57 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
And you get the unexpected charactr error when you read the psf? I am not sure you can append a PSF without one being present already.
This seems to be a PSF for just biotin, and I think it is a very good idea to see if this works before adding the peptide. The part of your script after reading the biotin pdb will not work in this case.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22701 11/03/09 04:47 PM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
I tried to use the inp file (b3.txt)that i've just attached and it generated a pdb file but the two part of segment remained separated. always because there is some problem in the coordinates but i don't understand where is the error (maybe in the IC SEED?)
I want thank to you so much again for your help

Attached Files
b3.txt (775 Bytes, 364 downloads)
b3.pdb (5.55 KB, 300 downloads)
Re: biotin parameters
FranciT #22702 11/03/09 08:52 PM
Joined: Sep 2003
Posts: 4,796
Likes: 2
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 4,796
Likes: 2
OK, let's backtrack.
You have RTF and parameter files with topology and parameter data for biotin. You have a PDB for biotin. You want to have PSF, parameters and coordinates for BTN linked to the peptide GLY GLY GLY THR.
The logic would be to generate a PSF for BTN GLY GLY GLY THR in two segments since the default peptide links specified for amino acid residues would not be appropriate for BTN; add the BTN-GLY bond using the patch, and make sure that all angle and dihedral terms necessary for energy evaluations are generated (NB, this is unrelated to the IC tables!). Then read the actual coordinates for BTN from the pdb, and construct the peptide coordinates using the IC table data in the RTF. A simple model but possibly useful.
Something along the following lines should work:
* Generate PSF and coordinates for BTN GLY GLY GLY THR
*
read rtf card name ....
read para card name ...
read seque btn 1
gene btn
read seque card
* the peptide part
*
4
GLY GLY GLY THR
gene pept setup first none
patch link btn 1 pept 1 setup
autogenerate angles dihedrals
! Now we have the PSF. Read coordinates for biotin
read coor pdb name btn.pdb
! Build rest of structure using IC table information
ic para
! No need for IC seed since the BNT part has coordinates
! The LINK patch must have an IC table connecting the two parts
ic build
hbuild sele hydrogen end
print coor
energy
write psf card name btn-pept.psf
* BTN GLY GLY GLY THR from rtf ... and para ...
*
write coor card name btn-pept.crd ! Use CHARMM files for all real work, PDB only if absolutely necessary
* BTN GLY GLY GLY THR from biotin PDB and CHARMM IC build for the peptide
*

Note the absence of the following features in the script:
stream
charmm variables
bomlev
open unit
close
numerous blank lines
anything else unrelated to the specific task of creating the PSF and the coordinates

This is to enhance readability, understandability and chances of getting help.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: biotin parameters
lennart #22706 11/04/09 11:54 AM
Joined: Oct 2009
Posts: 31
FranciT Offline OP
Forum Member
OP Offline
Forum Member
Joined: Oct 2009
Posts: 31
thank you very much again for your help and support, i will work on it i will say to you if at the end everything will work.
thank you again

Re: biotin parameters
FranciT #23302 02/02/10 06:50 PM
Joined: Jan 2010
Posts: 1
S
Forum Member
Offline
Forum Member
S
Joined: Jan 2010
Posts: 1
Would you be able to provide the reference for these parameter and topology files vis a vis biotin? I would like to be able to cite the source. Thanks a lot.
-Sheldon

Page 1 of 2 1 2

Moderated by  alex, lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.018s Queries: 58 (0.011s) Memory: 1.0802 MB (Peak: 1.2936 MB) Data Comp: Off Server Time: 2020-10-25 03:01:31 UTC
Valid HTML 5 and Valid CSS