[gmx-users] Missing terminal cap group

[anu chandra]

Dear Justin,

Thanks for the reply. I just had a recheck of Gromacs Charmm36ff provided
in Grocmacs website (
http://www.gromacs.org/Downloads/User_contributions/Force_fields).
Unfortunately ACE group is missing in the .rtp file and also, in the .n.tdb
file. But, it is present in the Chramm27ff, which came with Gromacs package
itself. The Charmm36ff provided by
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs also have the ACE
group in the .rtp file. Is it okay if I replace the charmm36ff in
gromacs/share/gromacs/top/ folder ( downloaded from
http://www.gromacs.org/Downloads/User_contributions/Force_fields ) with the
one from MacKerell lab?

Many thanks
Aneesh

On Fri, Jul 3, 2015 at 4:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/3/15 11:10 AM, anu chandra wrote:
>
>> Dear Gromacs users,
>>
>> I am trying to generate topology for a membrane protein, which is capped
>> with acetyl and methyl amide group, using Charmm36 force field in Gromacs.
>> Unfortunately, the acetyl (ACE) group is seems to be missing in the
>> Gromacs
>> Charmm36 force field. Can anybody suggest me a way to add acetyl group
>> with
>> Charmm36 force field?
>>
>>
> The ACE capping group is present in the force field .rtp, so it's not
> missing. If it's not in your coordinate file, then you need to build it
> with some external software.  The GROMACS website has some suggestions for
> that.
>
> -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.
>