[gmx-users] Non Standard residues moving Away

[Justin Lemkul]

On 8/7/17 3:01 PM, Souvik Dey wrote:
> Hi,
> 
> Grompp is running successfully without any errors. But my protein and
> ligands are very far away from each other. So, what I fear is that the
> interactions among them may not be well accounted for by MD simulations.
> 

If the coordinates that came out of your topology generation program are 
incorrect, then it is pointless to use them.  Use the original coordinates from 
the bound complex.  No sense wasting time with a fruitless simulation when you 
already had usable coordinates.

-Justin

> On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> 
>> Hi,
>>
>> The only thing that matters is the order of the molecules, residues and
>> atoms, and preferably naming. These must match between topology and
>> coordinates when you eg use grompp. The point of doing an MD simulation is
>> generally to keep the topology constant while changing the coordinates. So
>> give grompp whatever file in whatever format suits you, subject to the
>> above constraint.
>>
>> Mark
>>
>> On Mon, 7 Aug 2017 16:25 Souvik Dey <souvik.dey29 at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I am trying to simulate a Protein Ligand system. Now, my system has some
>>> non standard residues and I standardized them for AMBER forcefield using
>>> ACPYPE. However, when I assemble the gro files of the Proten generated
>> from
>>> pdb2gmx and the gro files obtained from ACPYPE, I see that they are not
>>> situated next to each other. They have have moved far away.
>>>
>>> Now, is there any trick by which the coordinates of the PDB file do not
>>> change while being converted into a gro file or is there any way to
>> restore
>>> the previous condition of the PDB file?
>>>
>>> Thanking you,
>>> Souvik Dey
>>>
>>> --
>>> Souvik Dey
>>> Integrated Science Education & Research Centre
>>> Visva Bharati University
>>> Santiniketan-731235
>>> West Bengal
>>> 8981736643
>>> --
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> 
> 
> 

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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