[gmx-users] converting pdb of protein+ATP+water+ion into gromacs files

[Dina Mirijanian]

got it.  Thanks Justin.


On Wed, Oct 23, 2013 at 4:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/23/13 4:28 PM, Dina Mirijanian wrote:
>
>> Hello,
>> I am trying to convert a protein+ATP+water+ion system pdb into gromacs
>> files.  I need to use the existing water and ion coordinates.  I can
>> convert the protein part using pdb2gmx and grompp fine.  But, I do not
>> know
>> how to process the solvent and ion coordinates separately and combine them
>> to make the final system.  Can anyone give me direction?  I am new to
>> gromacs...
>>
>
> Copy and paste the coordinates into the pdb2gmx-processed coordinate file
> (note that you can keep .pdb format or convert to .gro easily with
> editconf).  The solvent and ion topologies are #included in the
> pdb2gmx-produced topology already, you just need to update the [molecules]
> directive accordingly.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
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