I am trying to run a md stimulation in gromacs for HDAC2 inhibitor and ligand. The protein is metalo protein, contain a Zn atom. Now I am facing problem whille running the nvt.mdp file. I have attached the error details. It will be very helpful if anyone can solve this error.
David Bickel
Subhadeep Sen Can you share the *.mdp file? My guess is that the groups defined in the "tc-grps" parameter, do not include your Zn ion.
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Subhadeep Sen
Thank you sir for your response. Can you suggest how to add the An ion in the .mdp file. And I will share the .mdp file definitely.
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Riya Samanta
Subhadeep Sen, it would be great if you could share the MDP file. Here, I think you need to form a group to include the missing atom and then include that in Tc_groups. Thanks!
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