Hi Simon Kao,
I have attached parameter files for heme. Parameters are modified based on following papers
J. Physc. Chem. B 2008, 112, 8165-8173
Proteins: Structure, Function, and Bioinformatics 62:1074-1087 (2006)
Hope it will be useful to you
Regards
Abdul Rajjak
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of SimonKao
Sent: Saturday, March 27, 2010 4:41 AM
To: amber.ambermd.org
Subject: [AMBER] Amber:antechamber & heme(metal?) problems
Jason and Bill, thanks for your emails!
I found the tutorial & examples of using antechamber, and I followed the steps.
But some errors happened again in antechamber.
First I separate HEM from 2dn1.pdb, as a new pdb file.
Then I attempted to run antechamber using this file with following script also shown in Amber9 manual:
> antechamber -i hem1.pdb -fi pdb -o hem1.mol2 -fo mol2 -c bcc
The error message is shown below.
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/package/chem/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit
I already checked some mails in the archives, and I noticed that antechamber does not deal with metal ions.
Some replies said, I need to create the ion as a residue in leap, and provide parameters for other atom types.
Am I right?
I shall be very thankful for any more details of suggestions or comments in this regard.
Best regards,
---------------------------------END--------------------------------------------
Kao
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- application/octet-stream attachment: HEME.pdb
Received on Sun Mar 28 2010 - 23:30:03 PDT
