[gmx-users] impropers in Gromacs and acepype tool
chetanvm10 at gmail.com
Thu Mar 6 23:42:59 CET 2014
I think acepype Amber2gromacs tool has amber parameter files. but here is
On Thu, Mar 6, 2014 at 4:40 PM, Chetan Mahajan <chetanvm10 at gmail.com> wrote:
> Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have
> just one .top file which contains topologies and parameters. Just curious:
> where to get Amber parameter set from?
> On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 3/6/14, 5:16 PM, Chetan Mahajan wrote:
>>> I just wanted to check the order of atoms in a improper in gromacs input
>>> file *.top. According to urea example on page 137 ( section 5.7)of manual
>>> 4.6.4, order of i,j,k,l atoms in improper always starts with central
>>> whereas that in a *.top file generated with acepype lists i,j,k,l order
>>> improper in formate ion as H O C O. Central atom at third position. Is
>>> right or bug in the tool acepype?
>> It's right. The example in the manual is for Gromos force fields. You
>> should look at the actual .rtp files for the AMBER parameter set you're
>> trying to use. Suffice it to say that different atom orders are supported,
>> because the Gromacs machinery (specifically pdb2gmx) knows how to deal with
>> lots of stuff based on bonded geometry.
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> 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.
More information about the gromacs.org_gmx-users