<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 help. I could run the EM with ATP in its right place. But position restrained dynamics gives warnings saying that some angles are rotated beyond 30 deg. So when i directly went for MD run it is running fine. What dis-advantages i have of not performing position restrained dynamics on my ATP-receptor complex system ?<br><br>Regards,<br>Nikhil<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> Tuesday, 23 June, 2009 12:35:12 PM<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,<br>> We can use max 4 coloumns for naming atoms. But .rtp file has 5 coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now the error is "atom N not found in residue 1ATP while combining tdb and rtp"<br><br>pdb2gmx tries to cap termini of peptides automatically, but this isn't a peptide. So look at pdb2gmx -h and choose the option that will allow you to interactively choose that no terminal capping needs to take place.<br><br>Mark<br><br>> ------------------------------------------------------------------------<br>> *From:* Mark Abraham <<a ymailto="mailto:Mark.Abraham@anu.edu.au"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Tuesday, 23 June, 2009 11:16:26 AM<br>> *Subject:* Re: [gmx-users] simulation of protein in presence of ATP<br>> <br>> nikhil damle wrote:<br>> > 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>> You've broken the PDB format, which encodes the information in fixed-column style. See <a href="http://www.wwpdb.org/documentation/format32/v3.2.html" target="_blank">http://www.wwpdb.org/documentation/format32/v3.2.html</a><br>> <br>>
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