<div dir="ltr">Hi Nahren,<br>Thanx for your help, I opened the pdb file with swisspdb viewer and then tried the pdb2gmx command over that pdb file and got the following error.<br><br>Total mass 28295.072 a.m.u.<br>Total charge 1.000 e<br>
Writing topology<br>Processing chain 5 'E' (372 atoms, 9 residues)<br>There are 0 donors and 0 acceptors<br>There are 0 hydrogen bonds<br>Warning: 'NDP' not found in residue topology database, trying to use 'NDPH'<br>
<br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 3.3.3<br>Source code file: pdb2gmx.c, line: 421<br><br>Fatal error:<br>Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms<br>
while sorting atoms<br>-------------------------------------------------------<br><br>and the error for the all atom forcefield were as follow.<br><br>-------------------------------------------------------<br>
Program pdb2gmx, VERSION 3.3.3<br>Source code file: resall.c, line: 436<br><br>Fatal error:<br>Residue 'NDP' not found in residue topology database<br><br>-------------------------------------------------------<br>
<br><br>any advice for this will be of great help for me.<br><br>Thanx,<br>Vivek<br><br><div class="gmail_quote">2008/8/12 nahren manuel <span dir="ltr"><<a href="mailto:meetnahren@yahoo.com">meetnahren@yahoo.com</a>></span><br>
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<div>Dear Vivek,</div>
<div>you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs.</div>
<div> </div>
<div>nahren<br><br>--- On <b>Tue, 8/12/08, vivek sharma <i><<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a>></i></b> wrote:<br></div>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;">From: vivek sharma <<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a>><br>Subject: Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens<br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Date: Tuesday, August 12, 2008, 6:34 PM<div><div></div><div class="Wj3C7c"><br>
<br>
<div>
<div dir="ltr">Hi David,<br>Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same?<br>whether swiss pdb can help in such cases?<br>
<br>With Thanx,<br>Vivek<br><br><br><br>
<div class="gmail_quote">2008/8/12 David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" rel="nofollow" target="_blank">spoel@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<div></div>
<div>vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi There,<br><br>I am new to molecular dynamics and GROMACS.<br>While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command....<br>
<br> pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce<br><br>I got the following in the last of error.....<br>......<br>......<br>......<br>.......<br>N-terminus: NH3+<br>C-terminus: COO-<br>
WARNING: atom CE2 not found in residue 270 while adding atom<br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 3.3.3<br>Source code file: genhydro.c, line: 304<br><br>Fatal error:<br>
Atom CE2 not found in residue PHE270 while adding hydrogens<br>-------------------------------------------------------<br> I tried the same with different force field and water models, but getting the same error again and
again.<br>any suggestion will be highly appreciated.<br></blockquote><br></div></div>You have an incorrect pdb file. An atom is missing. You have to fix it yourself.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br><br>With thanx,<br>Vivek<br><br>------------------------------------------------------------------------<br>
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