[gmx-users] Query- Ligand topology

[Justin Lemkul]

On 3/15/15 3:58 PM, Priya Das wrote:
> Thankyou for the reply .
> I tried to generate topology using Swiss Param website.
> <http://www.swissparam.ch/>
> Its somewhat trustworthy it seems.
>
> The only difference is that each 45 atoms of the ligand has unique charge
> group number.
> The assigning of charges are justified.
>

The phrases "somewhat trustworthy" and "charges are justified" do not seem 
compatible :)

As someone who develops force fields, I tend to be a stickler here.  You have to 
know what the assumptions are in the model, what the target data are, and 
determine how well the force field matches those target data.  Simply relying on 
"the server gave me something that kind of looks reasonable" is really bad 
justification when a reviewer wants to know how you parametrized your ligand.

If you haven't validated the parameters against some target data (for CHARMM, 
start with QM molecule-water interactions and QM energy scans for bonded 
parameters, see e.g. the CGenFF paper), then you can't say with any confidence 
how good the parameters are.

Compare with what the ParamChem server gives you; it provides a penalty score 
showing you where refinement needs to be done.  It's at least a quantitative 
estimate to help you improve the parameters.

-Justin

> *I have still a small query : Has the atom name in .itp file and .gro file
> has to be same?*
>
> On Sun, Mar 15, 2015 at 5:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/15/15 6:50 AM, Priya Das wrote:
>>
>>> Dear all,
>>>
>>> I am submitting a ligand with 45 HETATM PDB file in PRODRG, but i get a
>>> result with 46 HETATM.
>>> The main error is in the -NH group, the structure generated by PRODRG
>>> shows
>>> four valence for Nitrogen.
>>>
>>
>> Changing protonation states is covered in the PRODRG FAQ.
>>
>>   Is there any other tool/option for generating the topology?
>>>
>>>
>> For GROMOS, try ATB.  At the very least, you need to be carefully
>> scrutinizing and re-optimizing the PRODRG charges and charge groups.  The
>> output is generally not very accurate.  Never trust a black box with
>> something so crucial :)
>>
>> -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
>>
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>
>
>

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

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

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