[gmx-users] pdb2gmx with GROMOS

Dries Van Rompaey dries.vanrompaey at gmail.com
Fri Feb 19 09:50:26 CET 2016

Hi Justin,

Sorry for the late reply. Haven't had a chance to look at this yet. Could
you post your output files or compare the contents of yours to mine? I
chose Gromos 54a7 as my forcefield with the SPC water model. (command line
is gmx pdb2gmx -f 1aki.pdb).
I'd like to know if this is a cosmetic issue or if something else is going

My files can be found here:



On 1/20/16 3:48 AM, Dries Van Rompaey wrote:
>* Hi Justin and Marco,
*>>* Thanks for your reply. I get this behaviour when I specify the default NH3+
*>* and COO- termini through -ter, as well as when I don't use the -ter flag.
*>* Selecting the COOH terminus type removed the warning for the C-terminus,
*>* but selecting the NH2 terminus type did't remove the warning for the
*>* N-terminus. That's not a very physiological state, however.
*>>* Can anyone replicate this error?
I can't trigger the same with 5.1 or with current git master.  Try from a fresh
install and make sure no one has messed with your force field files.



More information about the gromacs.org_gmx-users mailing list