Hi Thomas,
I am not an Amber expert but I could help with my humble knowledge. can you
try the PDB file I created for you below for methylene chloride and see if
it runs fine:
HEADER LIG_
REMARK 6
HETATM 1 H1 LIG 1 1.475 0.264 1.035 1.00 0.00
HETATM 2 C1 LIG 1 0.884 0.058 0.139 1.00 0.00
HETATM 3 Cl1 LIG 1 1.142 1.357 -1.031 1.00 0.00
HETATM 4 H2 LIG 1 1.203 -0.888 -0.304 1.00 0.00
HETATM 5 Cl2 LIG 1 -0.821 -0.064 0.590 1.00 0.00
END
Hope it works fine, let me know the outcome
Best wishes
Mahmoud
On 3/24/11 5:42 PM, [1]thomas.fox.boehringer-ingelheim.com wrote:
Hi Dave,
here is a simple example, methylene chloride:
The pdb file is:
HETATM 1 C * 0 0.000 0.000 0.000 1.00 0.00
C
HETATM 2 CL * 0 1.773 0.000 0.000 1.00 0.00
CL
HETATM 3 H2 * 0 -0.363 0.727 0.727 1.00 0.00
H
HETATM 4 H3 * 0 -0.363 -0.993 0.266 1.00 0.00
H
HETATM 5 H4 * 0 -0.363 0.266 -0.993 1.00 0.00
H
CONECT 1 3 4 5 2
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1
END
The antechamber command:
antechamber -i test.pdb -fi pdb -o test.prepin -fo prepi
The resulting test.prepin:
0 0 2
This is a remark line
molecule.res
INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C c3 M 3 2 1 1.540 111.208 180.000 0.000000
5 H2 h1 E 4 3 2 1.090 70.554 -135.000 0.000000
6 H3 h1 E 4 3 2 1.090 70.551 -14.996 0.000000
7 H4 h1 E 4 3 2 1.090 70.551 104.996 0.000000
8 Cl cl M 4 3 2 1.773 180.000 90.000 0.000000
LOOP
IMPROPER
DONE
STOP
As you can see, the IGRAPH in the prepin file for the chloride has been
changed from CL -> Cl. It would be great if antechamber could be changed not
to reset the atom name...for the time being I have written a perl script to
read the atom names from the pdb file and replacing them in the prepin file.
Not very elegant, but it works.
All the best,
Th.
Mit freundlichen GrĂĽĂŸen / Kind regards,
Dr. Thomas Fox
Boehringer Ingelheim Pharma GmbH & Co. KG
Lead Identification and Optimization Sup
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585
[2]mailto:thomas.fox.boehringer-ingelheim.com
Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
Ralf Gorniak, Mark Hagmann, Michael Klein, Dr. Martin Wanning; Vorsitzender
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-----UrsprĂĽngliche Nachricht-----
Von: David A Case [[3]mailto:case.biomaps.rutgers.edu]
Gesendet: Donnerstag, 24. März 2011 14:24
An: AMBER Mailing List
Betreff: Re: [AMBER] Atom name convention/conversion in antechamber
On Wed, Mar 23, 2011, [4]thomas.fox.boehringer-ingelheim.com wrote:
when I process a pdb file with antechamber (Ambertools 1.4) to generate a
prepin file (am1bcc charges, gaff FF), I noticed that some atom names from
my
pdb file are changed during this procedure. In particular, two letter
halogen
(Cl, Br) names are converted from CL -> Cl and BR -> Br.
Can you send an example? I *think* this has been fixed in the developers'
tree, but my memory is sketchy, and we should double-check.
...thanks...dave
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[6]
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--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[9]
http://people.bath.ac.uk/mess20/
[10]
http://www.bath.ac.uk/person/812559
*********************************************
Mahmoud E. Soliman
Lecturer of pharmaceutical organic chemistry
Pharmaceutical Organic Chemistry Dept.
Faculty of pharmacy
Zagazig University
Zagazig
Egypt
**********************************************
Email:
[11]mess20.bath.ac.uk
[12]meelkot.zu.edu.eg
[13]mahmoudelkot.gmail.com
References
1. mailto:thomas.fox.boehringer-ingelheim.com
2. mailto:thomas.fox.boehringer-ingelheim.com
3. mailto:case.biomaps.rutgers.edu
4. mailto:thomas.fox.boehringer-ingelheim.com
5. mailto:AMBER.ambermd.org
6.
http://lists.ambermd.org/mailman/listinfo/amber
7. mailto:AMBER.ambermd.org
8.
http://lists.ambermd.org/mailman/listinfo/amber
9.
http://people.bath.ac.uk/mess20/
10.
http://www.bath.ac.uk/person/812559
11. mailto:mess20.bath.ac.uk
12. mailto:meelkot.zu.edu.eg
13. mailto:mahmoudelkot.gmail.com
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Received on Thu Mar 24 2011 - 09:30:02 PDT
