Dear Santanu,
My apologies that your original message never made it to the list. We seeing
more and more examples of this of late. There is probably an overzealous
spam filter somewhere which is discarding messages. We are working to try
and track this down.
Anyway, in regards to your message. The divcon.out files gives a clue:
UNRECOGNIZED ELEMENTAL SYMBOL: DU
So divcon did not understand one of your atoms. Checking the divcon.in file
we see that all atoms are of type DU:
CARTESIAN AM1 STANDARD DIRECT OPT=BFGS XTEST=0.0001 CHARGE=0
created by wmopcrt() for divcon
1 du 35.4230 40.6750 60.9770
2 du 34.9850 41.1400 59.6560
3 du 35.1470 40.0030 58.6160
4 du 34.6960 40.4250 57.1980
5 du 34.3610 38.8740 59.0190
6 du 35.8280 42.3780 59.2540
7 du 37.0510 42.2870 59.2730
8 du 35.2350 43.4040 58.9610
END_COORD
Obviously not correct.This is most likely due to misreading of the pdb file.
So if we take a look at a couple of lines from your pdb file and compare
them to one from a pdb file from www.pdb.org:
HETATM 7 O DTH A1 317 37.051 42.287 59.273 1.00 23.79 O
HETATM 8 O2 DTH A1 317 35.235 43.404 58.961 1.00 25.82 O
ATOM 1 N SER A 1 4.951 -29.247 6.490 1.00 39.09
N
We can see the problem. Your pdb file does not conform to the pdb standard
which has fixed width field. Hence your atom numbers is in the wrong place,
as is your name, coordinates etc. Thus antechamber is most likely reading
the D of DTH as being the atom name and is translating this to a dummy atom
du. Thus if you fix the spacing in your pdb file it should work correctly.
Good, luck...
All the best
Ross
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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http://www.rosswalker.co.uk/> | PGP Key
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Dear Sir,
At first I sent this male to AMBER mail reflector, but
somehow it could not be sent.
So I am forwarding this mail to you. please help me to solve my problem
given below.
Regards
From: santanu roy <66.santanu.gmail.com>
Date: Feb 20, 2007 3:21 PM
Subject: about ANTECHAMBER
To: amber.scripps.edu
Dear Sir,
I am little bit in problem while handling with Antechamber
program . I wanted to use Antechamber to make a forcefield parameter for
DTH(D - Threonine) molecule. But it did not run showing some error. I am
attaching input and out files with this mail.
Please check these and guide me how solve this problem.
Thanking you,
Yours sincerely
Santanu Roy
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Received on Wed Feb 21 2007 - 06:07:42 PST
