Dear sir,
Thank you so much for your kind help. I have changed residue name as ARS
and its atom name as AS, I have given the cutoff in xyz.in 2.9, but the
residue MET is in the position 9.8 Angstrom away from As ion, but it is
still considering MET, and I am getting again an error given below.
It contains the residue 11-MET as sidechain coordinated.
It contains the residue 12-CYS as sidechain coordinated.
It contains the residue 13-CYS as sidechain coordinated.
It contains the residue 18-CYS as sidechain coordinated.
Totally there are 43 atoms in the small model.
Totally there are 185 electrons in the small model.
***Creating the standard model...
It contains the residue 11-MET as normal.
Traceback (most recent call last):
File "/home/camp/Desktop/Amber14/amber14/bin/MCPB.py", line 569, in
<module>
premol2fs, cutoff, watermodel, 2, largeopt, sqmopt, smchg, lgchg)
File "/home/camp/Desktop/Amber14/amber14/bin/mcpb/gene_model_files.py",
line 1742, in gene_model_files
bdedatms, libdict, autoattyp)
File "/home/camp/Desktop/Amber14/amber14/bin/mcpb/gene_model_files.py",
line 1319, in build_standard_model
attype = libdict[resname + '-' + atname][0]
KeyError: 'MET-AS'
I have attached xyz_small.pdb, please take a look at this, metal ion has
atom name AS but residue name changed to MET.
Regards,
Shilpa T
On Tue, May 30, 2017 at 10:39 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Sushi,
>
> As3+ is a special case, you need to have its Residue name as “ARS”, and
> its atom name as “AS” in the corresponding pdb and mol2 files.
>
> Please let me know whether it solves the problem.
>
> Kind regards,
> Pengfei
>
> > On May 29, 2017, at 7:35 AM, Sushi Shilpa <sushishilpa.gmail.com> wrote:
> >
> > Hi,
> >
> >
> >
> > I'm trying to use MCPB.py on a complex with a As and three CYS, but I am
> > receiving the error as shown below when the "MCPB.py -i xyz.in -s 1"
> > command is entered. I am using Amber 14 with AmberTools 15 on a Linux
> and
> > Python 2.7.
> >
> >
> >
> >
> >
> > The xyz.in file looks like:
> >
> >
> >
> > original_pdb xyz_fixed_H.pdb
> >
> > group_name xyz
> >
> > cut_off 4
> >
> > ion_ids 1
> >
> > ion_mol2files AS.mol2
> >
> > naa_mol2files AS.mol2 WAT.mol2
> >
> >
> >
> >
> >
> > The error message is as follows:
> >
> >
> >
> >
> > Totally there are 25 atoms in the sidechain model.
> > Traceback (most recent call last):
> > File "/home/camp/Desktop/Amber14/amber14/bin/MCPB.py", line 555, in
> > <module>
> > cutoff, watermodel, 2, largeopt, sqmopt, scchg, lgchg)
> > File
> > "/home/camp/Desktop/Amber14/amber14/lib/python2.7/site-
> packages/mcpb/gene_model_files.py",
> > line 1713, in gene_model_files
> > scresant, scresact, scresknh, screskco, scchg, outf, sqmopt)
> > File
> > "/home/camp/Desktop/Amber14/amber14/lib/python2.7/site-
> packages/mcpb/gene_model_files.py",
> > line 1214, in build_sidechain_model
> > AtNum = Atnum[gatm.element]
> > KeyError: 'A'
> >
> >
> >
> > Please help me to fix this issue.
> >
> >
> >
> > Regards,
> >
> > Shilpa T
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue May 30 2017 - 21:30:03 PDT
