[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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