Dear Amber Developers,
I'm planning to run simulations with pmemd.cuda in Amber16
using charmm force fields.
For this purpose, I used chamber in parmed (also in Amber16)
to convert charmm files to amber formats.
Then, I found that the TIP3P water is not properly handled,
yielding the message (output file)
Number of triangulated 3-point waters found: 0
and also the error message (stdout)
Hydrogen atom 2317 appears to have multiple bonds to atoms
2316 and 2318 which is illegal for SHAKEH.
This is not the first time for me to use pmemd.cuda with chamber
generated files, and indeed, when I did such simulations before
with Amber14, this problem did not occur.
Indeed, if I use chamber in Amber14 for the same charmm files, and
then run simulations with pmemd.cuda of Amber16, no error occurs
and SHAKE is properly applied.
So, the only difference between the successful and failure simulations
is in the use of
(1) chamber in amber16/bin/parmed,
(2) amber14/bin/chamber
(chamber is not present in amber16/bin)
I did some investigation on the topology files generated by the above
two different chambers, and I found that
(1) yields the amber topology in which the water residue name is TIP3
and water atom names are OH2, H1, H2 (charmm convention),
whereas
(2) yields the amber topology in which the water residue and atom
names are converted to WAT, O, H1, H2 (amber convention).
I'm not quite sure whether these differences are causing the problem,
but it's clear that some conversions which were done in chamber in
Amber14 are not done in chamber in parmed of Amber16.
Is this true?
Or, is there a way to solve this problem with parmed in Amber16?
At the moment, I'm using chamber in Amber14 ... but it's nice if I can
do everything using the tools in Amber16 only.
Best wishes,
Song-Ho Chong
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Received on Sun Sep 18 2016 - 09:30:03 PDT
