AMBER Archive (2002)

Subject: Carnal BUG??

From: William Wei (william_at_phm.utoronto.ca)
Date: Wed May 01 2002 - 22:19:03 CDT

Hi, Amber funs, I meet some problems with Carnal. Can anybody help me?
Here is my input and output by Amber7 carnal:

Input:
-------------------------------
FILES_IN
# Input the parm.top file, and the coordinates.
  PARM p1 parm.top;
  STREAM s1 mdcrd300_sim1.crd.Z
            MD_CMVMo_CnsP_1_1.5ns_mdcrd.Z
            MD_CMVMo_CnsP_1.5_1.8ns_mdcrd.Z
            MD_CMVMo_CnsP_1.8_2ns_mdcrd.Z
            MD_CMVMo_CnsP_2_2.3ns_mdcrd.Z
            MD_CMVMo_CnsP_2.3_2.5ns_mdcrd.Z
            MD_CMVMo_CnsP_2.5_3ns_mdcrd.Z
            MD_CMVMo_CnsP_3_3.5ns_mdcrd.Z
            MD_CMVMo_CnsP_3.5_4ns_mdcrd.Z;
  STATIC ref1 parm.crd;
FILES_OUT
# output the coordinates in OUTPUT
  COORD c1 Mono_Avg_50_4ns.pdb PDB;

  TABLE tab1 Tab_RMS_CA_Reser_Cry.tab;

DECLARE
  GROUP grp1 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-248)
                             |(RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 451-496)));
  GROUP grp2 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-248)));
  GROUP grp3 ((ATOM NAME CA)&((RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 451-496)));

  RMS fit1 FIT grp1 s1 ref1;
  RMS fit2 FIT grp2 s1 ref1;
  RMS fit3 FIT grp3 s1 ref1;

OUTPUT
  COORD c1 s1 AVERAGE ATOM 4200;

  TABLE tab1 MEAS;
END
-------------------------------
Output:

----------------------------------

                          - CARNAL -
                          AMBER 6.0

                      COORDINATE ANALYSIS

input Car_RMS_Ca_Crystal_4ns.in
> FILES_IN
> # Input the parm.top file, and the coordinates.
> PARM p1 parm.top;
Reading parm file (parm.top)
parm: opening parm.top
parm.top title:

> STREAM s1 mdcrd300_sim1.crd.Z
Using default parm (parm.top) for STREAM s1
 (box will be read from stream)
> MD_CMVMo_CnsP_1_1.5ns_mdcrd.Z
> MD_CMVMo_CnsP_1.5_1.8ns_mdcrd.Z
> MD_CMVMo_CnsP_1.8_2ns_mdcrd.Z
> MD_CMVMo_CnsP_2_2.3ns_mdcrd.Z
> MD_CMVMo_CnsP_2.3_2.5ns_mdcrd.Z
> MD_CMVMo_CnsP_2.5_3ns_mdcrd.Z
> MD_CMVMo_CnsP_3_3.5ns_mdcrd.Z
> MD_CMVMo_CnsP_3.5_4ns_mdcrd.Z;
stream: opening MD_CMVMo_CnsP_1_1.5ns_mdcrd.Z
stream: opening MD_CMVMo_CnsP_1.5_1.8ns_mdcrd.Z
stream: opening MD_CMVMo_CnsP_1.8_2ns_mdcrd.Z
stream: opening MD_CMVMo_CnsP_2_2.3ns_mdcrd.Z
stream: opening MD_CMVMo_CnsP_2.3_2.5ns_mdcrd.Z
stream: opening MD_CMVMo_CnsP_2.5_3ns_mdcrd.Z
stream: opening MD_CMVMo_CnsP_3_3.5ns_mdcrd.Z
stream: opening MD_CMVMo_CnsP_3.5_4ns_mdcrd.Z
stream: opening mdcrd300_sim1.crd.Z
> STATIC ref1 parm.crd;
Using default parm parm.top for STAT ref1
stat: opening parm.crd
stat: read in 41681 atoms plus box
> FILES_OUT
> # output the coordinates in OUTPUT
> COORD c1 Mono_Avg_50_4ns.pdb PDB;
>
> TABLE tab1 Tab_RMS_CA_Reser_Cry.tab;
>
> DECLARE
> GROUP grp1 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-249)
> |(RES 250-266)|(RES 273-285)|(RES
295-375)|(RES 395-441)|(RES 551-496)));
                             |(RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 551-496)));
............................................................................
......................^
Error in Car_RMS_Ca_Crystal_4ns.in line 1163075637: GROUP RES: range is
backward
    Last token was )
----------------------------------
I change the DECLARE GROUP grp1:

---------------
DECLARE
  GROUP grp1 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-248)|(RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 451-496)));
  GROUP grp2 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-248)));
  GROUP grp3 ((ATOM NAME CA)&((RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 451-496)));
.......
-------------

Then output:
--------------------------
.......
> DECLARE
> GROUP grp1 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-249)|(RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 451-496)));
** Group grp1: 204 atoms
> GROUP grp2 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-249)));
** Group grp2: 204 atoms
> GROUP grp3 ((ATOM NAME CA)&((RES 250-266)|(RES 273-285)|(RES
295-375)|(RES 395-441)|(RES 551-496)));
  GROUP grp3 ((ATOM NAME CA)&((RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 551-496)));
............................................................................
......................^
Error in Car_RMS_Ca_Crystal_4ns.in line 1163075637: GROUP RES: range is
backward
    Last token was )
------------------------

Modifying:
----------------
......
DECLARE
  GROUP grp1 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-248)|(RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 451-496)));
  GROUP grp2 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-248)));
  GROUP grp3 ( (ATOM NAME CA)&((RES 250-266)|(RES 273-285)|(RES
295-375)|(RES 395-441)|(RES 451-496)) );
......
---------------
Output:
--------------
.......
> DECLARE
> GROUP grp1 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-249)|(RES 250-266)|(RES 273-285)|(RES 295-375)|(RES
395-441)|(RES 451-496)));
** Group grp1: 204 atoms
> GROUP grp2 ((ATOM NAME CA)&((RES 2-18)|(RES 25-37)|(RES 47-127)|(RES
147-193)|(RES 203-249)));
** Group grp2: 204 atoms
> GROUP grp3 ( (ATOM NAME CA)&((RES 250-266)|(RES 273-285)|(RES
295-375)|(RES 395-441)|(RES!451-496)) );
  GROUP grp3 ( (ATOM NAME CA)&((RES 250-266)|(RES 273-285)|(RES
295-375)|(RES 395-441)|(RES!451-496)) );
............................................................................
...............^
Error in Car_RMS_Ca_Crystal_4ns.in line 1380274977: GROUP RES: unexpected
token
    Last token was !
-------------------

The last time carnal add a "!" to my input. Anyone have the same experience?
Have a good night.

William.