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
setyanto tri wahyudi
-----------------------------------------
Departemen Fisika
Institut Pertanian Bogor
Gedung Wing-S (depan Gymnasium)
Kampus IPB Darmaga
16680
Telp/Fax. 0251-625728
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Received on Fri Jul 23 2010 - 04:00:03 PDT
