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
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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