[gmx-users] .itp file of choline molecule

soumadwip ghosh soumadwipghosh at gmail.com
Mon Dec 8 15:01:51 CET 2014

Dear Justin,
                Thank you so much for your help. I saw the lipid_topper.str
files you mentioned about. But I have some questions. Am I supposed to
install CHARMM 36 in my source code with those tar.gz files and then modify
the atomtypes? Currently I am using CHARMM 27 force field and I wrote the
problem I encountered. Where do I get my choline.pdb file? I saw the
atomtypes mentioned over there . Do you want me to change the atomtypes in
the atomtypes.atp of my CHARMM 27 ff directory and then do pdb2gmx to
obtain the choline.top ? As suggested by you, I understand thet there was
some problem with my initial pdb file. Are the topology parameters listed
in the link compatible with all the versions of CHARMM? My questions might
sound very stupid but I dont have much experience of working with topology
building. It will be really helpful for me to understand if you suggest me
what is to be done step wise.

Thanks for your time in advance.

Soumadwip Ghosh
Research fellow
Indian Institute of Science, Bombay

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