Dear Dr. Ross Wlaker
It is really nice to hear from you.
Here is the command line I used:
antechamber -i G1a.mol2 -fi mol2 -o G1b.mol2 -fo mol2 -j 1 -at AMBER
A part of the output is attached here:
9 I9 -3.5480 1.0650 0.0000 F 1 MOL 0.035151
10 I10 -1.7910 -2.1570 0.0000 F 1 MOL 0.010279
11 I11 1.8170 -2.1410 0.0000 F 1 MOL -0.013250
12 I12 3.5420 1.0940 0.0000 F 1 MOL 0.055702
On the other hand, assigning gaff atom type gives the correct atom types:
antechamber -i G1a.mol2 -fi mol2 -o G1b.mol2 -fo mol2 -j 1 -at GAFF
9 I9 -3.5480 1.0650 0.0000 i 1 MOL 0.035151
10 I10 -1.7910 -2.1570 0.0000 i 1 MOL 0.010279
11 I11 1.8170 -2.1410 0.0000 i 1 MOL -0.013250
12 I12 3.5420 1.0940 0.0000 i 1 MOL 0.055702
All the calculations were performed using AMBER_TOOLS1.4
Thanks so much for your interest.
Sincerely;
M. Ibrahim
On Wed, Jun 1, 2011 at 6:37 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Mahmoud,
>
>> I am writing today to report an error in AMBER_Tools.
>> Assigning the atom types of iodo-molecules according to "-at AMBER"
>> gives "Fluoride, F" for " iodine atoms, I".
>> Hope you could create a bugfix for this error, I had to repeat a work
>> of six months because of this tiny error.
>> Thanks in advance, and thanks for this powerful mailing list.
>
> Can you post the exact commands you ran here and the relevant files one
> would need to exactly reproduce this. You do not even mention which 'tool'
> from AMBER 'toolS' you are referring to here. I assume you mean Antechamber?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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>
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--
Mahmoud A. A. Ibrahim
Current Address
7.05, School of Chemistry,
The University of Manchester,
Oxford Road, Manchester, M13 9PL,
United Kingdom.
Home Address
Chemistry Department,
Faculty of Science,
Minia University,
Minia 61519,
Egypt.
Contact Information
Email: m.ibrahim.compchem.net
Website: www.compchem.net
Fax No.: +20862342601
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Received on Wed Jun 01 2011 - 11:30:03 PDT
