<div dir="ltr">Hi Justin,<br>Thanx for your suggestion. But, I am not getting how to do correction in those files I am using gromacs 3.3.3 and 1XU9.pdb molecule for my simulation.<br>I am not getting what is happening in the simulation...:(...:(<br>
kindly suggest.<br><br>With Thanx,<br>Vivek<br><br><br><div class="gmail_quote">2008/8/13 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;">
There are two potential solutions to this error. For background, refer to:<br>
<br>
<a href="http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database" target="_blank">http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database</a><br>
<br>
So your options are:<br>
<br>
1. If the ligand is present in the .rtp file, make sure your atom nomenclature corresponds to that of the force field.<br>
2. Remove the ligand and deal with its topology separately (search Google for John Kerrigan's tutorial for enzyme-ligand systems).<br>
<br>
-Justin<br>
<br>
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;"><div class="Ih2E3d">
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>
any advice for this will be of great help for me.<br>
<br>
Thanx,<br>
Vivek<br>
<br></div>
2008/8/12 nahren manuel <<a href="mailto:meetnahren@yahoo.com" target="_blank">meetnahren@yahoo.com</a> <mailto:<a href="mailto:meetnahren@yahoo.com" target="_blank">meetnahren@yahoo.com</a>>><div class="Ih2E3d">
<br>
<br>
Dear Vivek,<br>
you just have to download swisspdb and open your pdb file. Thats all<br>
you got to do and It is more than enough. If you have more than 2/3<br>
residues missing then, make sure the Ramachandran plots are fine.<br>
Also try a simple minimization before begining gromacs.<br>
nahren<br>
<br>
--- On *Tue, 8/12/08, vivek sharma /<<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a><br></div><div class="Ih2E3d">
<mailto:<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a>>>/* wrote:<br>
<br>
From: vivek sharma <<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a><br></div>
<mailto:<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a>>><div class="Ih2E3d"><br>
Subject: Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found<br>
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></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><div class="Ih2E3d"><br>
Date: Tuesday, August 12, 2008, 6:34 PM<br>
<br>
<br>
Hi David,<br>
Thanx a lot again. can you please tell me the criteria or the<br>
standards to do such correction or can you suggest some link or<br>
tutorial for the same?<br>
whether swiss pdb can help in such cases?<br>
<br>
With Thanx,<br>
Vivek<br>
<br>
<br>
<br>
2008/8/12 David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a><br></div>
<mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>><div class="Ih2E3d"><br>
<br>
vivek sharma wrote:<br>
<br>
Hi There,<br>
<br>
I am new to molecular dynamics and GROMACS.<br>
While trying MD for 1XU9.pdb (pdbid) in the very 1st<br>
step on using the command....<br>
<br>
pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp<br>
-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<br>
models, but getting the same error again and again.<br>
any suggestion will be highly appreciated.<br>
<br>
<br>
You have an incorrect pdb file. An atom is missing. You have<br>
to fix it yourself.<br>
<br>
<br>
<br>
With thanx,<br>
Vivek<br>
<br>
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="Ih2E3d"><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<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.<br>
Use the www interface or send it to<br>
<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="Ih2E3d"><br>
Can't post? Read<br>
<a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="Ih2E3d"><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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><br>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use<br>
the www interface or send it to<br>
<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="Ih2E3d"><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
_______________________________________________<br></div>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="Ih2E3d">
<br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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></div>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="Ih2E3d">
<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="Ih2E3d"><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="Ih2E3d"><br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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 href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></blockquote>
<br><div class="Ih2E3d">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
_______________________________________________<br></div><div><div></div><div class="Wj3C7c">
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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 href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br></div>