Re: Minimization error

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Dec 07 2016 - 11:36:44 CST

Hi Santanu,

See the users guide: http://www.ks.uiuc.edu/Research/namd/2.12b1/ug/node14.html. Especially note that "Constraints, restraints, and settles are not implemented in NAMD." The .top file you generated has positions restraints defined in all likelihood, which is why NAMD is complaining. Position restraints in NAMD are handled through a separate mechanism.

-Josh

On 12/06/2016 10:05 PM, Santanu Santra wrote:
Hi all,
         I am doing Namd simulation using gromos 43a1 ff for a protein in water medium. I have generated *.gro , topol.top , *.itp files using gromos 43a1 ff. But when I am trying to do minimization using these files in namd , I got the following error:

Warning: unknown mode position_restraints
Molecule Protein undefined.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: unexpected call to exit by user program. Must use CkExit, not exit!
Charm++ fatal error:
unexpected call to exit by user program. Must use CkExit, not exit!
Aborted (core dumped)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 I want to know from all of you if any thing is required to correct my error or the source of error. Any suggestion from anyone is highly appreciated.
Thanks in advance.
My .conf file is attached.

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