DME and Carnal with AMBER6

From: Katherine W. Abold <kabold_at_umich.edu>
Date: Tue 23 Apr 2002 10:48:04 -0400

I am having a problem with the DME function in Carnal in AMBER6. I am trying
to obtain essentially an RMS value for the Calpha atoms in my MD silumation
for comparison with the Bvalues in the crystal structure. The program
accepts the input file, but gives junk for an output. If anyone can please
explain the problem and how to fix it, I would greatly appreciate their
help. The sample in and out files follow.

Here is a brief in file:

FILES_IN
PARM p1 TP_TG0MC.prmtop;
STREAM si
SCanal_310EQ.restrt0251
SCanal_310EQ.restrt0000 SCanal_310EQ.restrt0252
SCanal_310EQ.restrt0001 SCanal_310EQ.restrt0253
.
.
.
SCanal_310EQ.restrt0002 SCanal_310EQ.restrt0254;
STATIC ref_set ref.restrt;
FILES_OUT
TABLE tbl BvalueCA1.dme;
DECLARE
GROUP grp2 ((ATOM NAME CA) & (RES 2));
GROUP grp3 ((ATOM NAME CA) & (RES 3));
GROUP grp4 ((ATOM NAME CA) & (RES 4));
GROUP grp5 ((ATOM NAME CA) & (RES 5));
GROUP grp6 ((ATOM NAME CA) & (RES 6));
GROUP grp7 ((ATOM NAME CA) & (RES 7));
.
.
.
DME dmeid2 grp2 si ref_set;
DME dmeid3 grp3 si ref_set;
DME dmeid4 grp4 si ref_set;
DME dmeid5 grp5 si ref_set;
DME dmeid6 grp6 si ref_set;
DME dmeid7 grp7 si ref_set;
DME dmeid8 grp8 si ref_set;
DME dmeid9 grp9 si ref_set;
.
.
.
TABLE tbl
 dmeid2
 dmeid3
 dmeid4
 dmeid5
 dmeid6
.
.
.
 dmeid367;
END

Here is the output:

All of my input is read correctly and the I get for actual output:
STREAM si: no more files/crds (iteration 500)
SUMMARY
--DME fit2: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit3: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit4: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit5: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit6: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit7: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit8: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit9: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit10: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
--DME fit11: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff min
nan0x7fffffff N 500
.
.
.
--DME fit367: avg nan0x7fffffff dev nan0x7fffffff max nan0x7fffffff
min nan0x7fffffff N 500

In addition, the output table which gives each individual DME value gives
only nan0x7fffffff values.

I appreciate any help or suggestions that can be given.

Thanks,



Katherine Abold
Graduate Student in Medicinal Chemistry
University of Michigan
kabold_at_umich.edu
Received on Tue Apr 23 2002 - 07:48:04 PDT