Hi, I sent this question some minutes ago, but the attached files were
wrong. Now I attach the correct information.
Dear Amber users and developers, I am working on a system involving a
protein and a small ligand, with parameters defined in the Charmm Force
field.
With PSFGEN (psfscript.psf below) I generated psf and pdb files
describing my system. Next, with VMD > Solvate I added water molecules
and generated new psf and pdb files, for the neutral solvated
simulation box.
After that I used Parmed (in Amber16) to generate prmtop and inpcrd
files.
But, when I run a minimization with these inpcrd and prmtop, I get the
following error:
"Error: A residue defined as a "fast 3-point water"
is not defined by a triangle of three bonds.
Residue 892 contains 2 bonds."
I attach the prmtop:
https://www.dropbox.com/s/uls70du3flbafgi/emc_neutr.prmtop?dl=0
and the psfscript.psf was:
package require psfgen
topology topo/top_all27_na.rtf
topology topo/top_all27_prot.rtf
topology topo/toppar_all27_na_nad_ppi.str
topology top_emc.inp
pdbalias residue HIS HSD
pdbalias atom ILE CD1 CD
segment U {pdb chainA_2.pdb}
segment Y {pdb chainD_2.pdb}
segment X {pdb nadpA.pdb}
segment Z {pdb emc.pdb}
coordpdb chainA_2.pdb U
coordpdb chainD_2.pdb Y
coordpdb nadpA.pdb X
coordpdb emc.pdb Z
guesscoord
writepdb emc_h.pdb
writepsf emc_h.psf
The commands I used in Parmed were:
chamber -psf ../solvate/emc_h_neutral.psf -crd
../solvate/emc_h_neutral.pdb -top ../topo/top_all27_prot.rtf -top
../topo/top_all27_na.rtf -top ../top_emc.inp -param
../topo/par_all27_prot.prm -param ../topo/par_all27_na.prm -param
../par_emc.prm -str ../topo/toppar_all27_na_nad_ppi.str -str
charmm-gui/toppar/toppar_water_ions.str -box bounding
Thanks in advance.
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Received on Thu Sep 07 2017 - 17:30:02 PDT
