[gmx-users] simulation of protein in presence of ATP

nikhil damle pdnikhil at yahoo.co.in
Tue Jun 23 07:11:26 CEST 2009


   Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb file attached herewith.

From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, 22 June, 2009 10:27:24 AM
Subject: Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote:
> Hi all,
>         I want to carry out a MD simulation of a receptor protein in presence of ATP molecule. ATP is included in .rtp file of ffG43a1 force field. but  post pdb2gmx, .pdb output file does not show crds of ATP. Does it mean that ATP is not recognized as a residue of protein in spite of being included in .rtp file. If so how does one carry out this simulation ? If .itp file of ATP is an option, how can one get the specific values of charges etc for constructing .itp file. Manual does not mention anything regarding it.

pdb2gmx only writes a single [moleculetype] section, plus possibly solvent, so it will not cope as you would wish with a coordinate file with protein and free ATP.

The format of a molecule .itp file is a subset of that for a .top file, so you can feed a separate coordinate file containing only ATP to pdb2gmx to get that .top file. Remove the inappropriate header and footer sections, and then #include this new .itp file in your original .top file appropriately, and adjust its [molecules] section correctly.

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