[gmx-users] pdb2gmx error

Sotirios Dionysios I. Papadatos si.papadatos at edu.cut.ac.cy
Wed Jul 8 10:34:56 CEST 2015

If I got it right I would suggest this. Try removing parts in your overall structure. 
For example let's say your system has 3 components water, ATP, TPO. Try removing all but water, try pdb2gmx, all but ATP ( like a sim in vacuo ) try once again pdb2gmx. This will make the "troubled" part "visible". 
As for the error message, this comes up when you are trying to simulate a molecule that is not included in the default molecule entries. So you will have to include it manually. But when you know which part produces the error then it will be much easier. 

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Saman Shahriyari <samanshahriyari at yahoo.com>
Sent: Sunday, July 5, 2015 10:06 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] pdb2gmx error

Dear Users
I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled structure holding ATP, water and TPO as hetero atoms. but I am faced with the following error. I checked all LUE residues (although I have got no residue with 28215089 number) and I found no missing atom N. I am really wondering what should be my next step. could you help me on this?
"Fatal error:Residue 28215089 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed."
Best regardsSaman
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list