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#176 - 10/21/03 04:40 AM Running CHARMM with ligands in proteins
tjaart Offline
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Registered: 10/16/03
Posts: 40
Loc: Pretoria, South Africa
Hi

I used to run CHARMM only on a protein without any ligands in. How do I insert a ligand? I already have a pdb file with the ligand in the correct position. I also made .crd, .psf and .rtf files with InsightII. When CHARMM reads in the pdb sequence will it recognise the ligand or do I have to put in a specific command for CHARMM to go and fetch the psf file during minimization?

Does anyone know of a tutorial which covers this subject?

Thanks!!
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Tjaart de Beer

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#177 - 10/21/03 08:22 AM Re: Running CHARMM with ligands in proteins [Re: tjaart]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
I am not familiar with the files produced by Insight, but if they are complete .psf and .crd files for your whole system all you need to do is:
* charmm script for protein+ligand
*
read rtf card name ...
read para card name ...
read psf card name my_system.pdf
read coor card name my_system.crd

If you have separate files for protein and ligand (eg, the files you get from Insight are just for the ligand) you need something like this:
* now with protein and ligand in different files
*
read rtf card name protein.rtf
read rtf card name ligand.rtf append
read param card name protein.prm
read param card name ligand. prm append
read psf card name protein.psf
read psf card name ligand.psf append
read coor card name protein.crd
read coor card name ligand.crd append
! use read coor pdb name .... if the coordinate files are in pdb format

The protein and ligand rtf and parameter files have to be compatible with each other (same atom types).
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#178 - 10/21/03 09:22 AM Re: Running CHARMM with ligands in proteins [Re: lennart]
tjaart Offline
Forum Member

Registered: 10/16/03
Posts: 40
Loc: Pretoria, South Africa
I get the following error when running CHARMM with ligand psf and crd files genrated by InsightII:

CHARMM> generate prot setu

***** ERROR in GENIC ***** Residue '^@^@^@^@ ' was not found.

What does the ***** ERROR in GENIC ***** mean? My ligand is called PTP. How do I make CHARMM accept it?

Thanks!!!!!!
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Tjaart de Beer

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#179 - 10/21/03 10:08 AM Re: Running CHARMM with ligands in proteins [Re: tjaart]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
The GENIC error you get indicates that there is a residue without a name ('^@^@^@^@' indicates an empty string) in your sequence.
How did you read in the aa-sequence of the protein? Which RTF are you using?


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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#180 - 10/21/03 10:28 AM Re: Running CHARMM with ligands in proteins [Re: lennart]
tjaart Offline
Forum Member

Registered: 10/16/03
Posts: 40
Loc: Pretoria, South Africa
CHARMM gets the sequence from the pdb file. I am using the RTF for my protein and ligand produced by InsightII. In which file would this empty string be?


Thanks!!!!!
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Tjaart de Beer

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#181 - 10/22/03 07:11 AM Re: Running CHARMM with ligands in proteins [Re: lennart]
jb007 Offline
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Registered: 09/30/03
Posts: 250
Loc: Florida State
While on the topic it seems like a good idea to create another forum for posting rtf's and param files concerning "unsusual" and/or non-standard CHARMM residues, although the appropriate forum might be found under "Parameter Set Discussion"...

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