[gmx-users] Re: Re: Fw: Re: Polymer-protein problem

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jan 24 08:28:13 CET 2010

On 24/01/10 18:02, P.R.Anand Narayanan wrote:
> Dear Sir,
> I energy optimised the polymer-protein structure using HYPERCHEM. The
> moment I created peptide bonds between them, the pdb was saved like the
> format mentioned previously. for eg;
> HETATM 1 N 1 -24.998 12.703 12.925
>  >
>  > HETATM 2 C 2 -24.749 12.813 11.460
>  >
>  > HETATM 3 C 3 -24.428 11.438 10.881
>  >
>  > HETATM 4 O 4 -25.267 10.544 11.131
>  >
>  > HETATM 5 H 5 -25.225 13.528 13.462
>  >
>  > HETATM 6 H 6 -25.636 13.216 10.970
>  >
>  > HETATM 7 H 7 -23.903 13.478 11.291
> So, if there is NO other way of using this type of pdb file in GROMACS;
> can you please suggest any other software where I can successfully make
> covalent bonds between the protein and polymer, optimise them under
> force-field algorithms and THEN use the pdb file in GROMACS?
> Eagerly awaiting your advise and reply!!!

It's perfectly possible to use the coordinates in this file, but you 
will have to do some legwork in re-assigning the residue names, or 
reading the HYPERCHEM documentation to disable this "feature". The PDB 
format is column-sensitive (look up the format description on their 
website), so if HYPERCHEM hasn't re-ordered the atoms, you might use the 
Unix tool cut to help generate files with correct left- and right-hand 
sides, and then the Unix tool paste to put them back together.

Frankly though, there's little purpose to doing EM on a ligand in 
HYPERCHEM. You can do that with GROMACS before or after you bind it to 
the protein. Starting from some ab initio in-vacuo minimum is next to 
irrelevant for doing solvated dynamics under an MM forcefield. Any 
structure that is vaguely plausible with respect to that forcefield will 
work fine for most purposes.

The real problem is generating the topology for use with GROMACS, since 
pdb2gmx requires that an .rtp entry exists. Search the wiki and mailing 
list - this issue has come up many times. Generating a topology for a 
structure that approximates the relevant amino-acid-polymer structure is 
often a good start. That can be adapted into an .rtp entry... but this 
is not a trivial topic and a good knowledge of chapter 5 of the GROMACS 
manual will be required.


>> >>"What program did you use to create this new PDB file? It looks like
> it severely
> crippled the file, changing just about everything about it. There is
> certainly
> no way to use this .pdb file, since there aren't even any residue names
> defined
> in it.
> -Justin"
> <<<<
> Thanking you,
> Regards,
> Anand
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