Dear Amber community, I am trying to run dynamics using pmemd.cuda. Using
psfgen I generated psf and pdb files describing the solvated system.
package require psfgen
topology ../prod_emc/topo/top_all27_na.rtf
topology ../prod_emc/topo/top_all27_prot.rtf
topology ../prod_emc/topo/toppar_all27_na_nad_ppi.str
topology ../prod_emc/top_emc.inp
pdbalias residue HIS HSD
pdbalias atom ILE CD1 CD
segment U {pdb ../prod_emc/chainA_2.pdb}
segment Y {pdb ../prod_emc/chainD_2.pdb}
segment X {pdb ../prod_emc/nadpA.pdb}
segment Z {pdb emc.pdb}
coordpdb ../prod_emc/chainA_2.pdb U
coordpdb ../prod_emc/chainD_2.pdb Y
coordpdb ../prod_emc/nadpA.pdb X
coordpdb emc.pdb Z
guesscoord
writepdb emc_h.pdb
writepsf emc_h.psf
In VMD I solvated and neutralized the system.
After that, used parmed to obtain the prmtop and inpcrd files.
Molecular dynamics runs were successful using sander and pmemd. But, when
I use pmemd.cuda I get the following error:
"205: 404 - 405 and 206: 405 - 406
Hydrogen atom 405 appears to have multiple bonds to atoms 404 and 406 which
is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters."
The indexes correspond to a residue of histidine. If atoms are numbered
starting from zero (VMD style), atom 405 is a hydrogen. But if the
numbering starts from 1, then atom 405 should be carbon. What numbering
style is used by pmemd.cuda?
Dropbox link with prmtop and psf files.
https://www.dropbox.com/sh/d03rnihlfxtb3bz/AABNGZ7qayAw64LxR5jkInNBa?dl=0
Thanks,
David.
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Received on Tue Sep 19 2017 - 23:00:02 PDT
