Dear Roopali,
The reason antechamber fails is quite clearly explained in the error
message:
"*Total number of electrons: 205; net charge: 0 *
INFO: Number of electrons is odd: 205
Please check the total charge (-nc flag) and spin multiplicity (-m
flag)"
I haven't checked your pdb, but your diphosphate probably has a formal
charge of -3 or so, so you should use antechamber with "-nc -3".
More importantly, however, antechamber/GAFF is not really meant for
parameterising ADP. Luckily, others (Carlson et al., 2003) have developed
parameters that should (at the very least) be a good starting point.
See here:
http://www.pharmacy.manchester.ac.uk/bryce/amber/
You can donwload the prepc and frcmod files for ADP and ATP from there.
Good luck,
Marc
On 3 June 2015 at 09:08, ROOPALI VERMA <roopaliverma7.gmail.com> wrote:
> *Dear Amber Users, *
>
> *I want to simulate a protein structure docked with ADP and for ADP want to
> generate its crd *
> *and top files. In order to do so I used ANTECHAMBER to generate its
> mol2 **file
> calculate the charges and atom types. I used the following command. *
>
>
> *root.drpunit-Precision-WorkStation-T3500
> :/home/drpunit/Desktop/interdomain/dockadp#
> antechamber -i ADP.pdb -fi pdb -o adp.mol2 -fo mol2 -c bcc -s 2 *
> *Running: /home/drpunit/amber12/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC
> <http://ANTECHAMBER_BOND_TYPE.AC> -f ac *
>
> *Running: /home/drpunit/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC <http://ANTECHAMBER_AC.AC> -p gaff *
>
> *Total number of electrons: 205; net charge: 0 *
> INFO: Number of electrons is odd: 205
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
>
>
>
> *Running: /home/drpunit/amber12/bin/sqm -O -i sqm.in <http://sqm.in> -o
> sqm.out *
> *Error: cannot run "/home/drpunit/amber12/bin/sqm -O -i sqm.in
> <http://sqm.in> -o sqm.out" of *
> *bcc() in charge.c, properly**, exit *
>
> Iam using Amber12 with Ambertools13.
> also attaching the pdb files of the ligand and the complex.
> what could be the possible reason.
>
> Please guide.
>
> Thanking in anticipation.
>
> Regards,
> Roopali
>
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Received on Wed Jun 03 2015 - 02:00:03 PDT
