From: Nan Li (nan.k.li2015_at_gmail.com)
Date: Mon Oct 26 2020 - 17:15:06 CDT
I am trying to use genpsf 2.0 and namd 2.14 to simulate a system with
halogen bondings, which involves bromine atoms, since I saw in the user
guide, genpsf 2.0 version is able to process halogen bonds. I am using the
force field from the latest version of CGenFF. However, in the psf file
from genpsf 2.0, I can only see there are bonds generated between the dummy
atom and the bromine atoms. When running simulations with Namd 2.14, I can
see in the output that namd is trying to get lonepair bonds from LPhost
entries. But the simulations crashed because the dummy atoms moved too
fast. Therefore, I don't see the halogen bonds were treated properly
because there is not LPhost entries in Psf file from genpsf 2.0.
I also tried to use genpsf 2.0 to get psf in Charmm format, which contains
a session "!NUMLP NUMLPH". I copied and pasted this session into the psf
file for namd. This time, I got the error message as "FATAL ERROR: must
have same number of LP hosts as lone pairs". It seems like the namd 2.14
can process "!NUMLP NUMLPH", but it requires the same number of LP hosts as
lone pairs?? But why? There are typically two LP hosts for one dummy atom.
Please instruct me how to proceed if you have successful experience with
modeling halogen lone pairs using namd 2.14.
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