[gmx-users] pdb2gmx with GROMOS

[Dries Van Rompaey]

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
on.

My files can be found here:
https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0

Thanks

Dries

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.

-Justin

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