Dear Prayagraj Fandilolu,
Thank you for your advise.
Now command works correct.
All the best,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
________________________________
From: Prayagraj Fandilolu <fprayagraj.gmail.com>
Sent: Thursday, July 13, 2017 12:42:44 PM
To: AMBER Mailing List
Subject: Re: [AMBER] antechamber problem
Dear Michael,
Kindly note the information given during running the job
Running: /var/spool/scratch/shokhen/amber16/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 231; net charge: 0
INFO: Number of electrons is odd: 231
Please check the total charge (-nc flag) and spin multiplicity (-m
flag)
you can adjust the charge and multiplicity of your molecule by putting the
-nc and -m flags respectively to your command.
As your molecule has a charge of -1, you can specify it in the command as:
antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 -nc -1
(-m 0)
This should solve your problem...
All the best!!!
Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
On Thu, Jul 13, 2017 at 2:45 PM, Michael Shokhen <michael.shokhen.biu.ac.il>
wrote:
> Dear Amber experts,
>
>
> I have on my server AMBER16 and AMBER TOOLS16.
>
> The ligand MS75 in my protein-ligand complex needs previous
> parametrisation by ANTECHAMBER.
>
> The MS75 ligand has a total charge -1.
>
> Applying original MOPAC2016 with AM1 hamiltonian I have calculated the MS75
>
> without any problem.
>
> Unfortunately, the standard AMBER command line:
>
>
> antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2
>
> returns with error message because the input MS75.pdb was incorrectly
> interpreted as having charge=0
>
> Running: /var/spool/scratch/shokhen/amber16/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Running: /var/spool/scratch/shokhen/amber16/bin/atomtype -i
> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 231; net charge: 0
> INFO: Number of electrons is odd: 231
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
>
> Running: /var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in -o
> sqm.out
> Error: cannot run "/var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in
> -o sqm.out" of bcc() in charge.c properly, exit
>
>
>
> The top of smq.in file automatically generated by bcc parameter in the
> antechamber command line
> demonstrates incorrect molecular charge definition based on input
> coordinates of the MS75.pdb:
>
> Run semi-empirical minimization
> &qmmm
> qm_theory='AM1', grms_tol=0.0005,
> scfconv=1.d-10, qmcharge=0,
>
>
> Could somebody advise me how to modify the command line
>
> antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2
>
>
> in order to setup the charge=-1 for MS75 ligand?
>
>
> Thank you,
>
> Michael
>
>
>
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>
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Received on Thu Jul 13 2017 - 03:30:02 PDT
