Tanping Li wrote:
Hey Justin,
Thanks for the help. I've generated big size of data so I hope I can find the
way to fix the problem before transfer to the new version.
I just find that it gives me problem when I use the self-defined atom type in
the state B, however works fine if I use the existing atom type in the state B.
I defined the atom types by the following way:
[ atometypes ]
;name mass charge Ptype C6 C12
dum_CH3 15.035 0 A 0 0
....
....
Did I missed some there? I noticed that the "at. num" is included in the
ffgmxnb.itp file. I searched the manual, but haven't find that.
It's the atomic number. Different force fields have their lines parsed
differently, unfortunately, so you have to adhere to the existing format. Add a
zero in the column for atom number and see if this improves the situation. I
would recommend not using ffgmx for anything, though. The newer manual gives
several reasons why it's a bad choice for just about any modern simulation.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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