[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Thu Nov 3 13:35:42 CET 2016

On 11/2/16 11:42 PM, Kingsley Theras Primus Dass . wrote:
> Hello users !
> I want to Add SO3- to tyrosine residue  of my protein. I generated the
> topology file for SO3- (TYS) residue using PRODRUG server and incorporated
> that topology into my topology. I am using GROMACS45a3 force field . but
> still when i try running pdb2gmx , it shows error.
> could you please suggest some solution for it .
> Program gmx pdb2gmx, VERSION 5.1
> Source code file:
> /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/resall.c,
> line: 486
> Fatal error:
> in .rtp file in residue TYS at line:
>      1         O     1  TYS       O     1   -0.682  15.9994

Looks like you've copied a line from an .itp file directly into an .rtp file. 
That won't work because the files have a fundamentally different format and 
purpose.  Spend some time in the manual reading about .rtp entries, and compare 
what you're doing to existing entries in the force field.

Don't use PRODRG parameters without validating and refining them.  They are 
suboptimal for MD simulations.




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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