[gmx-users] Re: converting pdb to gmx successfully - how?

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Feb 3 09:22:52 CET 2006

Hi David,

To interpret the number, note that pdb2gmx renumbers all atoms starting from

In addition, I don't know which force field you are trying to use, but you
may be best off with either OPLS or Amber. Then it may help to split the pdb
file and process the protein and DNA seperately. These can be easily
combined later on again. The long bonds usually arise because pdb2gmx
doesn't know where a chain starts and ends. It can infer that from a chain
identifier, but otherwise it will just connect residues in the order that
they are given. The long bond will then correspond to the break in chains or
it may be due to a stretch of missing residues. Then finally, -ignh is not
intended to ignore missing hydrogens, it is intended to ignore hydrogens
which should not be present according to the force field you're using, i.e.
strip all hydrogens and regenerate them again according to an idealized
geometry. The warnings about hydrogen atoms which should be there probably
arise because pdb2gmx fails to recognize them properly (as hydrogens).

Maybe it will also help if you have a look at the ff****.rtp file in the
Gromacs /share/top/ directory, which lists the residue definitions for a
given force field (ffG43a1.rtp for the gromos force field for example). In
addition, if you're using the Gromos force field you can try to get yourself
a Gromos manual, where all the building blocks are listed with the topology.

And if all else fails, you can post the output from pdb2gmx performed on the
DNA part and there will probably be someone who can help to see where it
goes wrong still.

Hope it helps,


On 2/2/06, David Mathog <mathog at caltech.edu> wrote:
> More progress, sort of.
> By changing C7 -> C5M in the DTHY records I finally managed
> to get pdb2gmx -ignh -missing to run to completion.
> That said, it does not appear to have worked correctly.
> 1.  None of the DNA is protonated.
> 2.  The protein is protonated
> which is craziness, it should be one way or the other.
> 3.  There were 3 long bond warnings right after "Making bonds...".
> However I cannot figure out why they are there since the
> corresponding atom positions in the gmx output file don't correspond
> to atoms that make bonds in the rtp file.
> What do the position numbers in the long bond message refer to?
> Thanks,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060203/c89f0f87/attachment.html>

More information about the gromacs.org_gmx-users mailing list