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AMBER Archive (2008)Subject: RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop
From: Ross Walker (ross_at_rosswalker.co.uk)
Hi Grange,
I'll try this out on my machine and see if I get the same problem. However,
Antechamber 1.27 used Divcon for the charge derivation which is newer and
You could try increasing the following in SIZES:
PARAMETER (MAXHEV=100, MAXLIT=100)
to 150 each and recompiling and see if that helps.
That said neither case is probably ideal. Doing charge fits on such large
1 GLU356 2 RESIDUE 4 B GLU 1 ROOT GLU B 356
2 GLU357 11 RESIDUE 4 B GLU 2 **** GLU B 357
3 VAL358 20 RESIDUE 4 B VAL 2 **** VAL B 358
4 ASP359 27 RESIDUE 4 B ASP 2 **** ASP B 359
5 CHU360 35 RESIDUE 4 B CHU 3 **** LEU B 360
6 GLU361 43 RESIDUE 4 B GLU 2 **** GLU B 361
7 ASP362 52 RESIDUE 4 B ASP 2 **** ASP B 362
8 AIB363 60 RESIDUE 4 B AIB 2 **** TYR B 363
9 CHV364 72 RESIDUE 4 B CHV 3 **** VAL B 364
10 ALA365 79 RESIDUE 4 B ALA 2 **** ALA B 365
11 ARG366 84 RESIDUE 4 B ARG 2 **** ARG B 366
12 PRO367 95 RESIDUE 4 B PRO 2 **** PRO B 367
13 ASP368 102 RESIDUE 4 B ASP 1 **** ASP B 368
So why would you want to use AM1-BCC charges and GAFF over a specific
Alternatively if you really want to use Antechamber and AM1-BCC charges then
All the best
Ross
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Hi,
I am getting an endless loop with AmberTools1.1 and 1.0 installations on
The command is:
antechamber -fi mol2 -fo prepi -i chp3.mol2 -o chp3.prepin -j 5 -c bcc -s 2
The chp3.mol2 is attached.
Perhaps one of the developers could execute this in their AmberTools
I have a tgz of the directory used for the run, and will send if anyone
Is a different means of reporting a possible bug recommended?
Thanks,
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