[gmx-users] n2t file format for similar atoms

[jwillcox at andrew.cmu.edu]

Okay, that sounds good.  Thank you!

Jon

>
>
> On 5/6/15 1:22 PM, jwillcox at andrew.cmu.edu wrote:
>> Hello,
>>
>> I'm trying to specify two different hydroxyl hydrogen atoms in the n2t
>> format:
>>
>> H    opls_988    0.435   1.0079 1    O 0.0945
>>
>> and
>>
>> H    opls_117    0.4238  1.008   1   O 0.1
>>
>> for a hydroxyl group on graphene and water, respectively.
>>
>> When performing x2top, it seems to assume all Hs in the system are
>> defined
>> by whichever set of parameters is listed first.  I tried using alternate
>> atom labels, e.g. HG and HW, but it gave the same problem.  Is there a
>> way
>> to separate the two different hydrogen types?
>>
>
> The simplest approach is to not use x2top for writing a water topology.
> It
> should be straightforward to write the water topology and #include it in
> the
> .top (or simply use one of the existing models).
>
> Likely what's happening is that x2top is matching the first instance of
> any H
> that matches the distance criterion (within 10% of the specified
> distance).  I
> bet if you reverse the appearance of the H lines in the .n2t, you'd get
> the
> opposite parameters assigned.  You could modify the x2top code to be more
> permissive if you like, but the simplest solution is what I said above -
> don't
> ask x2top to do something complex when the molecule isn't complex :)
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>