[gmx-users] Error : Atomtype not found

[Justin Lemkul]

On 1/7/15 6:29 AM, protim chakraborti wrote:
> Hello Folks,
>
> I am trying to run simulation of a metalloprotein, trying to find the
> interaction of metal ion with protein. I am using *"The Charmm27 force
> field and the tip3p water model".* I successfully ran the pdb2gmx and
> generated the resulting files. I am getting stuck when I run "grompp". The
> fatal error which comes is "Fatal error:Atomtype CU not found".
> I would also like to mention I made some changes at the rtp and itp entries
> pertaining to the force field. The last few lines of the pdb file is as
> follows.
>
> ATOM  11157  H   SER   752      -8.480   5.697   6.617
> 1.00480.00
> ATOM  11158  HG  SER   752     -10.013   3.169   9.799
> 1.00720.00
> ATOM  11159  HA  SER   752      -9.762   2.997   6.918
> 1.00480.00
> ATOM  11160 1HB  SER   752      -7.791   2.674   8.104
> 1.00720.00
> ATOM  11161 2HB  SER   752      -8.075   4.148   9.057
> 1.00720.00
> ATOM  11162 CU   CU    753      -3.345 -16.535   5.962  1.63 26.17
> END
> .....
>

Copper isn't present in CHARMM force fields, so unless you've parametrized it 
and added it correctly to all the necessary force field files (here, the error 
would be solved by adding parameters to ffnonbonded.itp), you should expect an 
error.

-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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