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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Received on Fri Jul 23 2010 - 05:30:04 PDT
