[gmx-users] pdb2gmx

Justin Lemkul jalemkul at vt.edu
Wed Jan 15 17:47:24 CET 2014

On 1/15/14, 10:06 AM, jwillcox at andrew.cmu.edu wrote:
> Hello,
> I was under the impression that pdb2gmx was supposed to referance the
> force fields as defined in oplsaa.ff/forcefield.itp, but it doesn't seem
> to be for me.
> To double check, I removed all force field parameters from forcefield.itp
> and pdb2gmx still ran and got the same result as before.
> How do I make pdb2gmx referance oplsaa.ff/forcefield.itp?

pdb2gmx doesn't do much of anything with forcefield.itp.  You tell it which 
force field you want to use, then it makes use of lots of files in that 
directory (see the manual for the list).  Most significant is the .rtp file. 
The #include statement for the force field is then simply written to the .top 
based on your selection.



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


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