Have you tried renaming your hydrogens in CH2CL2 to sth that doesnt start
with a H? Im not sure if the current implementation still identifies
hydrogens by their names, but this trick worked for me at some point in
ancient history...
Best,
Th.
Gesendet: Dienstag, 10. Oktober 2017 um 12:31 Uhr
Von: "Alain Chaumont" <chaumont.unistra.fr>
An: amber.ambermd.org
Betreff: [AMBER] pmemd.cuda and rigid CH2Cl2
Hi everyone,
I am currently running in a problem with pmemd.cuda.
I am simulating a Ti-complex in dichloromethane. CH2CL2 is represented by a
5 point rigid model.
When doing this I get the following error:
0: 280 - 283 and 2: 281 - 283
Hydrogen atom 283 appears to have multiple bonds to atoms 280 and 283 which
is illegal for SHAKEH.
0: 280 - 283 and 4: 282 - 283
Hydrogen atom 283 appears to have multiple bonds to atoms 280 and 283 which
is illegal for SHAKEH.
0: 280 - 283 and 5: 283 - 284
Hydrogen atom 283 appears to have multiple bonds to atoms 280 and 284 which
is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.
This corresponds to the first solvent molecule. I have seen in the AMBER
mailing list that this kind of problem appeared previously for water and
that this has been solved.
Has anyone an idea how this could be fixed with other type of solvents then
water? Or how to work around this?
Thanks in advance for the help
Best regards
Alain Chaumont
Dr. Alain Chaumont
Universitee de Strasbourg
UMR 7140
Laboratoire de Chimie Moléculaire de l’Etat Solide
4, rue B. Pascal
67008 Strasbourg
France
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Received on Fri Jan 12 2018 - 01:00:02 PST
