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Re: biotin parameters
FranciT #22696 11/03/09 11:38 AM
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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
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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
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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
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these are my files
thank you again

Attached Files
btn.pdb (2.58 KB, 438 downloads)
btn.psf (8.13 KB, 324 downloads)
b3inp.txt (832 Bytes, 352 downloads)
Re: biotin parameters
FranciT #22700 11/03/09 03:57 PM
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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
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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, 365 downloads)
b3.pdb (5.55 KB, 301 downloads)
Re: biotin parameters
FranciT #22702 11/03/09 08:52 PM
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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
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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
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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

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