Hi,
When g_disre reports restraint violations in the *.log file, what do the
restraint numbers correspond to?
If I have say 5 restraints in index groups 0 1 2 2 3 and g_disre reports
a violation on restraint 3 is is talking about index group 3 or the
third restraint in the file - in this cas
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds like the compatible problem
between GROMACS 3.3.2 and and UBUNTU 7.10. Both are rather new.
Herein I just suggest and hope others may help to install 3.3.2 on new
ubuntu 7.10
[EMAIL PROTECTED] wrote:
Bruce Milne wrote:
> You don't have to run pdb2gmx for the whole system at any point
Probably true.
> (it's
> not going to work anyway unless you add the POPC parameters to all the
> force field files and then add the POPC residu
Dear Adak,
[EMAIL PROTECTED] wrote:
Dear All;
when I try to run pdb2gmx command for making .top file of POPC+Protein, an
error appears: Residue 'POPC' not found in residue topology database.
I have copied all necessary .itp files in share folder and also in the path
where it is run.
what cou
Hi Vijay,
I've CC'd this email to the gmx-users as it's best to keep this on the list.
There doesn't seem to be any attached .mdp file with your email. Maybe
it got removed by my mail server.
If you are using ffG43a1 (Gromos96) then the sodium name should be NA+
with the charge included just
Hi,
What force field are you using? It may be that the sodium ion is named
differently e.g. NA instead of NA+. Check in the force field .atp file
for the correct name and make sure you use that in your .top file. Maybe
that's all that's wrong.
Cheers,
Bruce
Respected sir/madem,
i am usin
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