[gmx-users] charge correction in topology file from PRODRG

[Mahboobeh Eslami]

dear justin
thanks for your help




On Monday, December 9, 2013 1:44 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
 


On 12/8/13 6:18 AM, XAvier Periole wrote:
>
> For gromos ff you can also use the ATB server. From Alan Mark on Brisbane. It combine typography and non-bonded parameters all at once.
>
> It is not perfect but pretty good.
>

<shameless self-promotion>

For those wondering about some potential implications of topology errors and how 
to start going about fixing them, as well as an overview of some common QM 
calculations one can do to try to calculate charges for new groups: 
http://pubs.acs.org/doi/abs/10.1021/ci100335w

</shameless self-promotion>

-Justin

>> On Dec 8, 2013, at 8:27, Mahboobeh
 Eslami <mahboobeh.eslami at yahoo.com> wrote:
>>
>> hi all my friends
>> I use PRODRG and antechmber for building topology and coordinate files for my ligand separately.
>> i want to use GROMOS force field so i must to use the topology from PRODRG server. can i use the topology of antechamber for charge correction in topology fiel from PRODRG .
>> In general, are special principlesessential for charge correction in topology file from PRODRG
>>   thanks for your help
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
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


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