[gmx-users] fatal error in DNA-ligand simulation

[Justin Lemkul]

On 3/27/15 2:17 PM, marziyeh poshteh shirani wrote:
> Hi all
> I have the following error and I could not solve it after checking all
> the possible solutions on line.
> Thank you
> M.P.Shirani
>
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernaktoppush.c, line: 1166
> Fatal error:
> Atomtype CH2 not found
> These are SOL of line 1166-1168
>   92SOL     OW 1164   0.354   1.510   1.329
>   92SOL    HW1 1165   0.333   1.466   1.242
>   92SOL    HW2 1166   0.451   1.536   1.332
>

The quoted line number is in the source code file listed; it has nothing to do 
with the coordinate file.

You need to describe what it is that you're doing.  Either you've modified and 
broken the force field, or you're mixing force fields and using an incompatible 
atom type.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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