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

Justin Lemkul jalemkul at vt.edu
Wed Oct 23 22:37:43 CEST 2013

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 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 | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list