Hi, 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.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@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. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
ATP.pdb
Description: x-unknown/pdb
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