Re: amber-developers: Version 1.1 of AmberTools(?)

From: Volodymyr Babin <vbabin.ncsu.edu>
Date: Fri, 30 May 2008 12:38:48 -0400 (EDT)

Hi all,

the antechamber failures below are because of mine recent commits.
It is possible to get the tests PASSED by either the following:

Index: define.h
===================================================================
RCS file: /raid5/case/cvsroot/amber11/src/antechamber/define.h,v
retrieving revision 10.2
diff -u -r10.2 define.h
--- define.h 22 May 2008 04:22:01 -0000 10.2
+++ define.h 30 May 2008 15:25:29 -0000
.@ -28,7 +28,7 @@
 # define MAXBEED 20
 # define MAXATOMTYPE 250
 # ifdef NCSU_PENALTIES_H
-# define PSCUTOFF 33
+# define PSCUTOFF 10
 # else
 # define PSCUTOFF 10
 # define MAXVASTATE 8192

(reducing the PSCUTOFF), or regeneration of the .save files
using bondtype with PSCUTOFF=33. I do not entirely understand
the antechamber and hence have no clue which way is better.

Thank you & have a nice day,
  Volodymyr

> These tests are failing on an x86_64 using g95.
> The diffs may be due to recent src commits and no recent test commits:
>
> ./ambpdb_first_protein/first.pdb.dif
> ./ambpdb/restrt.pdb.dif
> ./ambpdb_first_rna/first.pdb.dif
> ./reduce/1ubqH.pdb.dif
> ./antechamber/chemokine/1b2t.mol2.dif
> ./antechamber/chemokine/1b2t.ac.dif
>
> ./ambpdb_first_protein/first.pdb.dif
> < ATOM 2 1H LYS 1 36.009 19.996 27.782 0. 0. 1 V
> ---
>> ATOM 2 H1 LYS 1 36.009 19.996 27.782 0. 0. 1 V
>
> ./ambpdb/restrt.pdb.dif
> < ATOM 1 H5T DA5 1 -0.521 -8.448 -2.584
> ---
>> ATOM 1 H5T DA5 1 -0.521 -8.448 -2.584 1.00 0.
>> H
>
> ./ambpdb_first_rna/first.pdb.dif
> < ATOM 2 O5* RG5 1 38.269 3.679 -21.201 0. 0. 1 B
> ---
>> ATOM 2 O5' RG5 1 38.269 3.679 -21.201 0. 0. 1 B
>
> ./reduce/1ubqH.pdb.dif
> 1c1
> < USER MOD reduce.3.10.070818 H: found=0, std=0, add=630, rem=0, adj=22
> ---
>> USER MOD reduce.3.13.080428 H: found=0, std=0, add=630, rem=0, adj=22
> 66,74c66,74
> < TURN 1 T1 THR 7 GLY 10 TYPE I
> 1UBQ 5
> ---
>> TURN *** T1 THR 7 GLY 10 TYPE I
>> 1UBQ 5
>
> ./antechamber/chemokine/1b2t.mol2.dif
> 1382c1382
> < 141 136 137 1
> ---
>> 141 136 137 2
>
> ./antechamber/chemokine/1b2t.ac.dif
> < BOND 141 136 137 9 CB SG
> ---
>> BOND 141 136 137 2 CB SG
>
> Once these are addressed we are probably ready to release.
>
> Scott
>
>
>
Received on Sun Jun 01 2008 - 06:07:59 PDT
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