[gmx-users] Charge on drug

[Justin Lemkul]

On 12/19/16 5:31 AM, tasneem kausar wrote:
> Thanks for reply
>
> I have visualized solvate.gro and em.gro. Some bonds that are not present
> in box.gro is seen in em.gro.
> I am giving you the link of the file to visualize.
> https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
> https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM

You have an amide group that distorts, bringing the carbonyl C closer to the 
amide proton, which VMD then fictitiously assigns as a C-H bond.  The C-N bond 
is much too short.  This suggests your topology is of insufficient quality for 
doing simulations and requires refinement.  There is, of course, no actual bond 
there, as Mark has pointed out.  Visualization software tries to guess where 
bonds should be based on interatomic distances.  The topology is definitive. 
What you see on your screen is not.

> I addition to that I have done energy minimization multiple times with
> steepest decent and conjugate gradient method. Potential energy value is
> negative in every minimization. When I am trying position restrain core
> dump with multiple lincs warning occurs.

Your topology needs work.  It will not be stable for any simulation.

-Justin

> Please tell me how this problem would be resolved
>
> On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Your energy minimization literally cannot create bonds because those are
>> already defined by your topology. See
>> http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#
>> Topology_bonds_vs_Rendered_bonds
>> for what's probably going on.
>>
>> Mark
>>
>> On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausar12 at gmail.com>
>> wrote:
>>
>>> Dear All
>>>
>>>
>>> I am using Acpype server to generate topology file of drug molecule to
>>> perform protein drug MD simulation. Acpype have generated the itp file
>> and
>>> other necessary for MD simulations. I am doing MD on gromacs 5.1.4
>> software
>>> using amber99sb force field. When I have done energy minimization some
>>> unwanted bonds are formed in drug molecule. So the position restraint is
>>> not able to execute. The problem is due to the unusual bond in drug atom.
>>> When I used the itp file of PRODRG server position restraint goes
>>> successfully. I have used the gromos54a7 ff. But there is problem with
>> the
>>> charge present on the atom that comes from PRODRG.
>>>
>>> Please tell me how charge on the atom can be corrected in itp file of
>>> PRODRG.  How the problem in energy minimization with the Acpype itp will
>> be
>>> resolved.
>>>
>>> Thanks in Advance
>>> With Regards
>>> Tasneem
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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

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