<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi,<br><br> 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.<br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Monday, 22 June, 2009 10:27:24 AM<br><b><span
style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] simulation of protein in presence of ATP<br></font><br>nikhil damle wrote:<br>> Hi all,<br>> 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.<br><br>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.<br><br>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.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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