[gmx-users] Problem with phenylglycine MD

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 15 08:53:58 CET 2006

Ashutosh Jogalekar wrote:
> Hello
> I am trying to run an MD on a short tripeptide contaning phenyglycine 
> (PHG)- that is with the phenyl ring direct attached to the alpha carbon. 
> I am using the OPLS force field. The peptide is (PHE-PHG-LEU)
> I modified the .rtp and .hdb files accordingly. I put in the atoms, 
> bonds, and improper dihedrals in the .rtp file. I put in the new name 
> PHG in the aminoacids.dat file.
> Everything seems to start ok, until I am done with the energy 
> minimization. There is no error, and the minimization ends smoothly. 
> However, at the end, the alpha carbon is distorted; it's not tetrahedral 
> and the hydrogen bends towards the phenyl ring. Not suprisingly, in the 
> rest of the simulation, the distortion is not relieved. I don't know 
> what's going wrong, since there is no error as such and the .rtp and the 
> .hdb files have been modified in an apt manner.
> One thing is that there are no parameters for some of the dihedrals in 
> the OPLS force field. So when I am doing grompp for the EM, the program 
> naturally puts zeros in front of those dihedrals. Two examples are:
> N  CA  CG CD1
> Could this be causing the carbon to distort? If so, where can I get the 
> parameters for these dihedrals?

Yes, the dihedrals and angles are the only forces involved in keeping 
the conformation tetrahedral. Are you sure you have described the 
Ha-Ca-Cg angle correctly?

For the dihedrals you may want to look at a similar dihedral, e.g. 

> Help will be really appreciated since I am stuck with this problem for 
> days!
> Thanks
> Ashutosh Jogalekar
> Emory University, Atlanta, GA
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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