[gmx-users] problem with phosphorylated serine

Justin Lemkul jalemkul at vt.edu
Tue Nov 18 01:00:29 CET 2014

On 11/17/14 6:55 PM, Jayant James wrote:
> Hi!
> Thanks it did work after I added "SEP    Protein" to the residuetypes.dat
> file. While executing pdb2gmx I found that I am asked to choose the water
> model and I choose SPC. Then I got the error that stating that (Error
> message below).
> Error Message
> -------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: pdb2gmx.c, line: 1879
> Fatal error:
> The topology file 'gromos43a1p.ff/spc.itp' for the selected water model
> 'spc' can not be found in the force field directory. Select a different
> water model.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Hence I went and listed the files in the non-phosphorylate and
> phosphorylated directories and found that many files in the
> non-phosphorylated directory are *not *present in the phosphorylated
> directory (given below)
> $ ls gromos43a1.ff/
> aminoacids.c.tdb  *aminoacids.vsd  * forcefield.doc   *spce.itp*
> aminoacids.hdb    atomtypes.atp    forcefield.itp   *spc.itp*
> aminoacids.n.tdb  ffbonded.itp     *ions.itp         tip3p.itp*
> aminoacids.r2b    *ff_dum.itp       methanol216.gro*  *tip4p.itp*
> aminoacids.rtp    ffnonbonded.itp  *methanol216.gro*  watermodels.dat
> $ ls gromos43a1p.ff/
> aminoacids.c.tdb  aminoacids.rtp   forcefield.doc  watermodels.dat
> aminoacids.hdb    atomtypes.atp    forcefield.itp
> aminoacids.n.tdb  ffbonded.itp     MD5SUM.txt
> aminoacids.r2b    ffnonbonded.itp  README
> SO MY QUESTION IS: Is it ok to copy these files that are missing in the
> phosphorylated force field directory from the non-phosphorylated
> force field directory?




Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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