[gmx-users] Charge on drug

[Justin Lemkul]

On 12/19/16 1:23 PM, tasneem kausar wrote:
> Thank you for reply
> What type of refinements are needed in topolgy file.
> I have created the topology file from pdb file. Mol2 was converted into pdb
> and sdf of pubchem was converted into mol2.
> So sdf to mol2 to pdb.
> And please suggest me the right choice of server for itp file generation.
>

Check the bond length parameters and make sure your coordinate file matches the 
order of the atoms in the topology.  Don't ignore warnings from grompp.

-Justin

> Thanks in advance
>
> On 19 Dec 2016 18:31, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>
>>
>>
>> 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
>>
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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

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