[gmx-users] Get a correct .pdb for a synthetic peptide

Sotirios Dionysios I. Papadatos si.papadatos at edu.cut.ac.cy
Wed Mar 8 10:36:38 CET 2017

Hi, to get things straight did you use pdb2gmx or just editconf? Where does the error occur?

My personal choice is Maestro which is free for academic use. The resulting pdbs' have no problem with Gromacs.

If you want to make minor changes, for example change LIG to DRG (assuming DRG is mentioned in the ff) then yes you can use a text editor.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of FL S <frank.leonard.schmidt at gmail.com>
Sent: Wednesday, March 8, 2017 11:01:13 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Get a correct .pdb for a synthetic peptide


I want to run a gromacs MD for a small synthesized peptide. All used amino
acids are known for and defined in gromacs, as are the termini.
Consequently it would be ideal to use pdb2gmx to create the*.gro, *.top and
*.itp, but I have troubles creating a syntactically correct *.pdb input

I created  *.pdb (or *.mol2) files using standard chemistry software such
as Chem3D and Avogadro, and also tried VMD and PRODMG, but never get a
*.pdb file readable by gromacs. Using editconf leads to a fatal error as
all atoms are assigned to residue DRG which is not defined. Using
swissparam for gives the same problem, just that now it is LIG, not DRG.
(and I ideally want to work with OPLS, not CHARMM). The only option I see
is to use an editor to manually change the atom numbering and to group the
atoms into amino acids, but this seems very tedious.

What is the usual “pipeline” you are using in order to create your own
molecular structure and import them into gromacs? Is there a tutorial?

I am working with gromacs 5.1.4 in a linux environment and am able to do
simulations using *.pdb input files downloaded from rcsb.org.

Thanks in advance
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