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
--
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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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