[gmx-users] Charge on drug

[tasneem kausar]

solvate.gro is box.gro file. It was typing mistake.

On Mon, Dec 19, 2016 at 4:01 PM, tasneem kausar <tasneemkausar12 at gmail.com>
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
> 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.
> 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/Visualizat
>> ion_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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>