[gmx-users] MD of methanol

[Mark Abraham]

On Tue, Feb 20, 2018 at 8:47 AM Adriano Santana Sanchez <
adriano.santanasanchez at kaust.edu.sa> wrote:

>
> 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.


The .top file can be made that way. But you can also make one in a text
editor in a couple of minutes, following the example in chapter 5 of the
reference manual, or any other .top file you have at hand. A methane
molecule from a pre-made .itp can be done in four lines.

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'?.
>>
>
That is the only way to make that approach work.


> 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?.
>>
>
Yes that's fine. But you may wish to follow all of
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

Mark

>
> 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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