Thank you Dr. Casr and Dr. Francois...
On Fri, Jul 23, 2010 at 7:28 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear setyanto tri wahyudi,
>
> You might look at R.E.DD.B.
>
> See http://q4md-forcefieldtools.org/REDDB/projects/W-43/
> up to W-49
>
> regards, Francois
>
>
>
>
> > Dear AMBER user and developer,
> >
> > I am trying to make organic solvent for my simulation. Here I will use
> > pentane, hexane, octane and decane aqueous.
> > For box preparation I use packmol, as suggested by Dr. David A Case.
> > But when make LEAP preparation i need Hexane paramerter.
> >
> > This is that i've been do it.
> >
> > I make hexane pdb file using PRODRG2 server (
> > http://davapc1.bioch.dundee.ac.uk/prodrg/)
> > this is inside pdb file : (pdb filename = hex2.pdb
> > ...................................................
> > REMARK
> > REMARK
> > REMARK This file was generated by PRODRG version 071121.0636
> > REMARK PRODRG written/copyrighted by Daan van Aalten
> > REMARK and Alexander Schuettelkopf
> > REMARK
> > REMARK Questions/comments to dava.davapc1.bioch.dundee.ac.uk
> > REMARK
> > REMARK When using this software in a publication, cite:
> > REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> > REMARK PRODRG - a tool for high-throughput crystallography
> > REMARK of protein-ligand complexes.
> > REMARK Acta Crystallogr. D60, 1355--1363.
> > REMARK
> > REMARK
> > HETATM 1 CAA DRG 1 5.340 -1.800 -4.370 1.00
> > 20.00 C
> > HETATM 2 CAB DRG 1 5.200 -1.210 -2.960 1.00
> > 20.00 C
> > HETATM 3 CAC DRG 1 4.220 -2.040 -2.130 1.00
> > 20.00 C
> > HETATM 4 CAD DRG 1 4.080 -1.450 -0.720 1.00
> > 20.00 C
> > HETATM 5 CAE DRG 1 3.100 -2.270 0.120 1.00
> > 20.00 C
> > HETATM 6 CAF DRG 1 2.960 -1.690 1.530 1.00
> > 20.00 C
> > CONECT CAA CAB
> > CONECT CAB CAA CAC
> > CONECT CAC CAB CAD
> > CONECT CAD CAC CAE
> > CONECT CAE CAD CAF
> > CONECT CAF CAE
> > END
> >
> -------------------------------------------------------------------------------------------------------------------
> >
> > then I use Antechamber program. This is my command
> >
> > $antechamber -i hex2.pdb -fi pdb -o hex2.mol2 -fo mol2 -c bcc
> >
> > but there were error
> >
> ------------------------------------------------------------------------------------------
> > For atom[1]:AA, the best APS is not zero, bonds involved by this atom are
> > frozen
> >
> > For atom[2]:AB, the best APS is not zero, bonds involved by this atom are
> > frozen
> >
> > For atom[3]:AC, the best APS is not zero, bonds involved by this atom are
> > frozen
> >
> > For atom[4]:AD, the best APS is not zero, bonds involved by this atom are
> > frozen
> >
> > For atom[5]:AE, the best APS is not zero, bonds involved by this atom are
> > frozen
> >
> > For atom[6]:AF, the best APS is not zero, bonds involved by this atom are
> > frozen
> >
> > The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic
> > double)Error: cannot run "/usr/local/amber10/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > judgebondtype() of antechamber.c properly, exit
> >
> -------------------------------------------------------------------------------------------------------
> >
> > I already try to make another pdb file using Avogadro, and marvinsketch,
> but
> > the same problem was apperaed.
> >
> > I also try to change -c bcc with other charge method, but error always
> > appear.
> >
> > I also try to find hexane parameter in amber archive reflector :
> > http://archive.ambermd.org/200302/0166.html, pu xuemei also have same
> need
> > with me.
> >
> > may somebody help me please, ?
> >
> > Thank you very much
>
>
>
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>
--
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Received on Sun Jul 25 2010 - 18:30:04 PDT
