My earlier email still applies: leap script, please.
Bill
On 9/7/17 5:14 PM, David Adrian Saez San Martin wrote:
> 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 - 17:30:03 PDT
