[gmx-users] Question regarding error

Marko Sever Marko.Sever at ki.si
Thu Nov 10 08:32:43 CET 2016

Why would such a command: 

gmx pdb2gmx -f system.pdb -i /home/bla/charmm36chol_psm_dopc.ff/PSM.itp -o systemprocessed.gro -water tip3p -ignh -ff charmm36chol_psm_dopc 

give me the following error:

Fatal error:
Residue 'PSM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

If I pointed it to the PSM.itp file?
What is the procedure to manually add the includes into the .top and yet generate the .gro file of the system? Is there any alternative to pdb2gmx or should I use that...
I got .itp files for the system from Charmm GUI.



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