[gmx-users] AMBER99 topology for ADP

[Justin Lemkul]

On 1/15/15 10:59 AM, Marc Hoemberger wrote:
> Thanks,
>
> I tried converting these so I can use them in GROMASC but I was unable to do so. Specifically I had troubles on how to convert the dihedral and “NONBON" parameters to GROMACS format.
>

There's probably more on this in the AMBER manual or their mailing list, but 
general format stuff is here:

http://ambermd.org/formats.html

Dihedral parameters are the multiplicity, force constants, etc.  The weird part 
is if there are any negative values that mean special things in their code.  The 
NONB section is just Rmin (or Rmin/2, again search their doc) and well depth, 
both of which are straightforward to convert to sigma/epsilon.

-Justin

> -Marc Hoemberger
> On Jan 15, 2015, at 10:39 AM, bipin singh <bipinelmat at gmail.com> wrote:
>
>> http://www.pharmacy.manchester.ac.uk/bryce/amber/
>>
>>
>> ------------------------------
>> Thanks and Regards,
>> Bipin Singh
>>
>> On Thu, Jan 15, 2015 at 7:48 PM, Marc Hoemberger <hoemberg at brandeis.edu>
>> wrote:
>>
>>> Hello,
>>>
>>> Does someone have the topology file of ADP for the AMBER forcefield?
>>>
>>> Best regards,
>>> Marc Hoemberger
>>>
>>> --
>>> 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.
>>>
>> --
>> 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.
>

-- 
==================================================

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

==================================================