Dear Dr. Ross Walker
As I believe, the mistake is in the following file:
amber10/dat/antechamber/ATOMTYPE_AMBER.DEF
Line 51:
ATD F * 53 1 &
The "F" should be "I"
Thanks again for your interest.
Sincerely;
M. Ibrahim
On Wed, Jun 1, 2011 at 7:15 PM, Mahmoud A. A. Ibrahim
<m.ibrahim.compchem.net> wrote:
> 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 |
>> ---------------------------------------------------------
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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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
>
--
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 - 11:30:04 PDT
