---------- Forwarded message ----------
Date: Fri, 23 Aug 2002 11:29:00 +0530 (IST)
From: Sanjeev B.S. <sanjeev_at_mbu.iisc.ernet.in>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: Carnal RMSDs
Hello,
I have 5 files and I need to sperately find four type of (fitted)
rmsds (Ca, backbone, all protien atom and system), all w.r.t. a reference
structure. Then I need to write them in five different files. But when I
do that I find RMSDs being much higher than they are shown by ptraj or
other tools. Could anyone let me know what is the mistake with the carnal
script please? I do not find any, and I am not sure it is a bug also.
Several of the scripts depend on carnal o/p so it will be nice if the
problem is sorted out. The scrpit is below.
Thanks in advance,
-Sanjeev
-----Carnal script--------------------------------------------------------
FILES_IN
PARM p1 ../promol.prm.top;
STREAM s1 ../../CRD/promol.0100_0200.crd.1 ;
STREAM s2 ../../CRD/promol.0100_0200.crd.2 ;
STREAM s3 ../../CRD/promol.0100_0200.crd.3 ;
STREAM s4 ../../CRD/promol.0100_0200.crd.4 ;
STREAM s5 ../../CRD/promol.0100_0200.crd.5 ;
STATIC ref_set ../promol.min.crd;
FILES_OUT
TABLE tbl1 promol.0101_0200.1.rms;
TABLE tbl2 promol.0101_0200.2.rms;
TABLE tbl3 promol.0101_0200.3.rms;
TABLE tbl4 promol.0101_0200.4.rms;
TABLE tbl5 promol.0101_0200.5.rms;
DECLARE
GROUP cal (ATOM NAME CA);
GROUP bkb (ATOM NAME N CA C);
GROUP all (SOLUTE);
GROUP sys (ALL);
RMS fit1.c FIT cal s1 ref_set;
RMS fit1.b FIT bkb s1 ref_set;
RMS fit1.a FIT all s1 ref_set;
RMS fit1.s FIT sys s1 ref_set;
RMS fit2.c FIT cal s2 ref_set;
RMS fit2.b FIT bkb s2 ref_set;
RMS fit2.a FIT all s2 ref_set;
RMS fit2.s FIT sys s2 ref_set;
RMS fit3.c FIT cal s3 ref_set;
RMS fit3.b FIT bkb s3 ref_set;
RMS fit3.a FIT all s3 ref_set;
RMS fit3.s FIT sys s3 ref_set;
RMS fit4.c FIT cal s4 ref_set;
RMS fit4.b FIT bkb s4 ref_set;
RMS fit4.a FIT all s4 ref_set;
RMS fit4.s FIT sys s4 ref_set;
RMS fit5.c FIT cal s5 ref_set;
RMS fit5.b FIT bkb s5 ref_set;
RMS fit5.a FIT all s5 ref_set;
RMS fit5.s FIT sys s5 ref_set;
OUTPUT
TABLE tbl1 fit1.c fit1.b fit1.a fit1.s;
TABLE tbl2 fit2.c fit2.b fit2.a fit2.s;
TABLE tbl3 fit3.c fit3.b fit3.a fit3.s;
TABLE tbl4 fit4.c fit4.b fit4.a fit4.s;
TABLE tbl5 fit5.c fit5.b fit5.a fit5.s;
END
Received on Mon Aug 26 2002 - 14:51:12 PDT
