[gmx-users] MD of methanol

[Adriano Santana Sanchez]

Hi Mark,

Thanks you for your email.  If I have a '.pdb' and '.itp' file but no
topology file I still need to make one and this is done
with either pdb2gmx or x2top. If for any reason the residue name is not
found on the database and it fails then the
only way I can think of is to add a manual entry to the 'aminoacids.rtp'?.

In any case, if someone wants to add an entry to the 'aminoacids.rtp' there
is nothing wrong with it provided it is
properly added, right?.

Thanks,
Adriano




-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: Tuesday, February 20, 2018 10:24 AM
To: gmx-users at gromacs.org
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] MD of methanol

Hi,


If you have an .itp then you have no need of editing an .rtp file that is
only used by pdb2gmx. That the simulation is unstable is unrelated, and we
don't have enough information to suggest why. Please do make sure you
understand how the pieces work, eg by trying the tutorials if you have not
already done so.

Mark

On Tue, Feb 20, 2018, 07:52 Adriano Santana Sanchez <
adriano.santanasanchez at kaust.edu.sa> wrote:

> Hi,
>
> I am trying to run energy minimization of a methanol molecule.
>
> I have a .pdb file of a single MeOH molecule and a  methanol.itp file 
> with parameters for the OPLSAA force field.
>
> I have added an entry for this '.itp' into 'aminoacids.rtp' putting 
> [atoms] [bonds].
>
> I can create a topology file this way but the simulations are unstable.
> What am I missing?.
>
> Thanks,
> Adriano
>
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