[gmx-users] Acpype topolgy error
Abid Channa
abid_channa04 at yahoo.com
Mon Feb 29 10:52:00 CET 2016
Dear Gromacs users,
I am going to run complex simulation. I have prepared ligand topology through acpype , from where I have taken two files .gro and .itp file. I have used Gromos ff for my simulation . I got atom type error while running this command " gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr". My acpype taken .itp file is like [ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 ca 1 THA C1 1 -0.119000 12.01000 ; qtot -0.119
2 ca 1 THA C2 2 -0.173300 12.01000 ; qtot -0.292
3 ca 1 THA C3 3 0.430600 12.01000 ; qtot 0.138
4 ca 1 THA C4 4 -0.182300 12.01000 ; qtot -0.044
5 ca 1 THA C5 5 -0.105000 12.01000 ; qtot -0.149It gave following error
Fatal error:
Atomtype ca not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Kindly suggest me How can I resolve this problem.
Thanks
Abid Ali Channa,
Junior Research Fellow,
Lab No. P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
International Center for Chemical and Biological Sciences (ICCBS),
University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. (309)
Cell # +923013553051.
http://www.iccs.edu/
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