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