Dear Fabian,
You might try R.E.D. Server Development at
http://q4md-forcefieldtools.org/REDS-Development/
Prepare a PDB input file for each molecule
if the total charge of a molecule is different from zero provide the
corresponding value(s) in the Project.config file such as:
MOLECULE1-TOTCHARGE = -1
MOLECULE2-TOTCHARGE = 1
Create an archive file:
tar zcvf archive.tgz Mol_red1.pdb Mol_red2.pdb
or
tar zcvf archive.tgz Mol_red1.pdb Mol_red2.pdb Project.config
upload the archive to R.E.D. Server Development
download the PXXXXX job
cd PXXXXX/Data-R.E.D.Server/Data-Default-Proj/
tleap -f leaprc.ff13q4mdfft
regards, Francois
> I am trying to use antechamber for a drug, which works great for one
> molecule, but if I use a pdb with two copies of the molecule,
> antechamber never ends:
>
> antechamber -i ritonavir_2mol.pdb -fi pdb -o ritonavir_2mol.mol2 -fo
> mol2 -c bcc -s 2
> Running: /Users/fabian/TOOLS/amber/amber12/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> ---Judge bond type for Residue 1 with ID of 1 and Name of RIT ---
>
> ---Judge bond type for Residue 2 with ID of 2 and Name of RIT ---
>
> Running: /Users/fabian/TOOLS/amber/amber12/bin/atomtype -i
> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 768; net charge: 0
>
> Running: /Users/fabian/TOOLS/amber/amber12/bin/sqm -O -i sqm.in -o sqm.out
>
> What is the right approach for this problem?
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Received on Sun Mar 30 2014 - 10:30:03 PDT
