What force field are you using in NAMD prior to Amber and what force
field are you planning to use in Amber for the mmpbsa calculations ?
If you do not have ff parameters for the methylated histidine compatibe
with the Amber ff, you need to generate them before. If there are
parameters published in the literature, you can just load those.
Hope this helps
Vlad
On 7/11/23 01:10, Ramachandran, Balajee via AMBER wrote:
> Dear all
>
> I have performed the mds in namd and have .dcd file. The aim of the study is to compute free energy (mmpbsa). The complex contains methylated histidine, and adp. When converting from NAMD to Amber, it doesnt recognizes the bond between the histidine NE2 and CH3. In addition to this, how to convert the ADP from namd to amber since we assign through GAFF in amber.
>
> Could anyone please suggest how to convert this complex from NAMD to compute in Ambertools.
>
> Your suggestions are welcome!
>
> Thanks and regards
>
> Balajee
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--
Dr. Vlad Cojocaru (PD, Habil.)
----------------------------------------------
Guest Scientist / Fmr. Project Group Leader
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
----------------------------------------------
Email: vlad.cojocaru.mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Tue Jul 11 2023 - 01:00:02 PDT
