There are no hydrogens on your PDB. You would first have to decide on
protonation and tautomer state and then add the hydrogens
accordingly. For nucleotides though I would recommend to use AMBER's
DNA/RNA force field and add building blocks if necessary. ADP
parameters have been developed earlier and best approach would be to
take tested ones from the literature and/or look in a database e.g.
http://www.pharmacy.manchester.ac.uk/bryce/amber/ or R.E.D.
On Wed, 3 Jun 2015 13:38:00 +0530
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
