[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Tue Nov 8 11:59:05 CET 2016

On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote:
> Hello users!!
> I generated a Topology file for SO3- using ATB topology generator , which
> is compatible with GROMACS. Then I copied the .rtp file from ATB and pasted
> it into  GROMACS aminoacid.rtp.
>  The  partial charge of aminoacid sulfated-tyrosine was -1.
> When I run -pdb2gmx there was error saying the atoms were missing ,
> -------------------------------------------------------
> Program gmx pdb2gmx, VERSION 5.1
> Source code file:
> /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2top.cpp,
> line: 1584
> Fatal error:
> There were 6 missing atoms in molecule Protein_chain_D, if you want to use
> this incomplete topology anyhow, use the option -missing
> then I ran pdb2gmx -ignh -p topol.top -missing
> It generated the topology file. But the parital charge of sulfated tyrosine
> was changed to -2, coz of missing hydrogen atoms.
> can you please suggest some solutions , to overcome this problem.

Add an .hdb entry for your residue so that pdb2gmx will build the missing atoms. 
  In general, never use the -missing option.



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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