[gmx-users] Ligand covalently bound to protein: Best practice

[Justin Lemkul]

On 5/21/15 4:51 PM, Ebert Maximilian wrote:
> Thanks for your comment and sorry for my weird english. I must have been in my thoughts :).
>
> I was also wondering if I attach covalently a protein to another protein or a large organic molecule through a residue in the middle of the sequence my approach would not work. Does anyone have a suggestion how setup a system like this?
>

Why won't your approach work?  The answer to this question is always the same: a 
modified residue in a biopolymer requires a modified .rtp entry.  The details of 
how that works depends on the force field, but the net effect is the same.  For 
linking proteins, that's what specbond.dat is for.  The parametrization details 
depend on the kind of linkage.  Isopeptides, disulfides, etc. are already 
handled easily.  Other things require more effort.

-Justin

> Thanks,
> Max
>
>
>> On May 21, 2015, at 4:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 5/21/15 4:30 PM, Ebert Maximilian wrote:
>>> Hi there,
>>>
>>> I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice?
>>>
>>
>> Sounds reasonable.
>>
>> -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

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