Dear List,
I have a trajectory and a gro file from GROMACS (with opls and tip4p force
fields). I am trying to use gromber in parmed however, it cannot convert
these files to amber. It gives the following error "InputError: AmberParm
does not support all of the parameters defined in the input Structure".
I tried using Intermol to perform the same conversion but it complains
"WARNING 2017-07-19 10:37:25 Can't convert to AMBER unless GROMACS is also
selected
INFO 2017-07-19 10:37:25 Finished!"
Is there a way to work around this problem? I want to use cpptraj commands
to perform analyses. While I can convert the trajectory to pdb, this gives
rise to another issue such as residue numbering (i.e. > 10000 residues).
Cpptraj can take .trr files as input but I was wondering whether the
residue numbering is taken into account when using a pdb as topology file.
Thanks,
Neha
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Tue Jul 18 2017 - 18:00:03 PDT
