Re: [AMBER] Antechamber

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Tue, 17 Sep 2013 16:20:58 +0200

Dear Jasim,

See a quick output generated by R.E.D. Python for your molecule:
http://q4md-forcefieldtools.org/Help/Jasim/

Your PDB input file:
http://q4md-forcefieldtools.org/Help/Jasim/Mol_red1.pdb

The structure was _optimized_ by QM using the Gaussian program & HF/6-31G*:
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Mol_m1/JOB1-gau_m1-1.out

Please compare the optimized geometry to your input molecule - it
looks like you used a TS structure within Antechamber & not a minimum;
from the complex within the protein this seems correct, but it might
be important to 'know' that the complexed ligand is not a minimum...

Two orientations are automatically generated for MEP computation:
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Mol_m1/JOB2-gau_m1-1-1.gjf
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Mol_m1/JOB2-gau_m1-1-2.gjf

The RESP inputs:
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Mol_m1/input1_m1
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Mol_m1/input2_m1

The FF lib you are interested in:
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Mol_m1/Mol_m1-o1.mol2
The total charge is corrected for rounding off errors:
Loading Mol2 file: ./Mol_m1-o1.mol2
Total unperturbed charge: 0.000000

The frcmod files:
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Data-Default-Proj/frcmod.known
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Data-Default-Proj/frcmod.correspondence (to be
extended)
The FF parameters it might be interesting to look at:
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown

The leaprc script, that loads the FF lib:
http://q4md-forcefieldtools.org/Help/Jasim/Data-R.E.D.Server/Data-Default-Proj/leaprc.ff13q4mdfft

regards, Francois


Comments below:

> The commands that I used are:
>
> nohup $AMBERHOME/exe/antechamber -i LIG.pdb -fi pdb -o LIG.prepin
> -fo prepi -c bcc -s 2 &

I do not think this input structure is a minimum...

> $AMBERHOME/exe/parmchk -i LIG.prepin -f prepi -o LIG.frcmod

not needed when sourcing gaff (below)?

> $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>
> source leaprc.gaff
>
> loadamberprep LIG.prepin

charge UNK
Total unperturbed charge: 0.000998

-> this is a strange total charge and I do not think this has to do
with a rounding off error

> loadamberparams LIG.frcmod

is it needed?

> model=loadpdb complex.pdb

check that the residue & atom names in the PDB file match these in the
FF lib (LIG.prepin)

> addions model Na+ 0
>
> saveamberparm model vac.prmtop vac.inpcrd



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Received on Tue Sep 17 2013 - 07:30:03 PDT