[gmx-users] converting pdb of protein+ATP+water+ion into gromacs files
dmirij at brandeis.edu
Thu Oct 24 00:44:51 CEST 2013
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:
>> 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
>> 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
> 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 A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
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