[gmx-users] problem while running grompp command

[Justin A. Lemkul]

rashi parihar wrote:
> Hi all.
> I am doing dynamics studies of protein-ligand dynamics.When I am running 
> grompp command error is coming "atomtype SDMSO NOT FOUND" . I checked in 
> drg.itp file
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OM 1 LIG OXT 1 -0.758 15.9994
> 2 C 1 LIG C 1 0.362 12.0110
> 3 OM 1 LIG O 1 -0.758 15.9994
> 4 CH1 1 LIG CA 1 0.154 13.0190
> 5 NL 1 LIG N 2 0.590 14.0067
> 6 H 1 LIG H3 2 0.001 1.0080
> 7 H 1 LIG H4 2 0.002 1.0080
> 8 H 1 LIG H1 2 0.002 1.0080
> 9 CH2 1 LIG CB 2 0.109 14.0270
> 10 CH2 1 LIG CG 2 0.109 14.0270
> 11 SDMSO 1 LIG SD 2 0.974 32.0600
> now in 11th row SDMSO IS PRESENT.How can I solve this problem?plz help me!!!
> 

The problem is that your topology file is calling "SDMSO," which does not exist. 
  All Gromos force fields use "SDmso" - capitalization matters.  Check the .atp 
file for your chosen force field to be sure of the requirements of the force field.

It looks to me like this is a PRODRG output.  Please see the paper linked from 
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips as to why you 
should likely not use this topology in its current state for anything.

-Justin

> -- 
>  
> images[12]
>  
> “Many Smiles Begin Because Of Another Smile . . . ."
>  
> Regards,
> Rashi
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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