[gmx-users] Regarding creating a itp for molecule from CGenFF

[Justin Lemkul]

On 6/23/17 1:02 AM, Dilip H N wrote:
> Hello all,
> 
> I want to simulate methylamine with amino acid misture in CHARMM FF, so i
> have created methylamine in mol2 format and created the .itp and .pdb files
> from the CGenFF (which creates itp in CHARMM FF for GROMACS). and i have
> included it in topology file also as:-  #Include "methylamine.itp", have
> solvated the system,
> But if i give the command for energy minimization:-
> gmx grompp -f em.mdp -c abc.gro -p topol.top -o em.tpr
> i am getting the error as
> 
> NOTE 1 [file em.mdp]:
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>    your simulation.
> 
> Setting the LD random seed to -1252943664
> Generated 85052 of the 85078 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 55198 of the 85078 1-4 parameter combinations
> 
> ERROR 1 [file Dimethylamine.itp, line 9]:
>    Atomtype 7 not found
> 
> How can i solve these error..??
> 

Integers aren't valid atom types, so something in your ligand topology is 
complete garbage.

-Justin

-- 
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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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