Hi amber users,
I am trying to do a rmsd calculation between my initial non-minimized
structure of the protein and the subsequent minimized structures (at
different steps in the minimization procedure). I am trying to use carnal
for this just to learn how to use it but I keep on getting an error
message. I did try to build the input file for carnal according to the
example in the amber manual (those files are also pdb). The pdb files I am
refering to in the input file are obtained from restart files using the
ambPdb command.
Here is my input file:
FILES_IN
PARM p1 polyAT_vac_Hmin.prmtop;
STREAM s1
min_gb.pdb
fixit.pdb;
FILES_OUT
TABLE tab1 rms_to_start;
DECLARE
RMS r1 FIT gALL s1;
OUTPUT
TABLE tab1 r1;
END
And the error message:
input stdin
> FILES_IN
> PARM p1 polyAT_vac_Hmin.prmtop;
Reading parm file (polyAT_vac_Hmin.prmtop) parm: opening
polyAT_vac_Hmin.prmtop
> STREAM s1
> min_gb.pdb
Using default parm (polyAT_vac_Hmin.prmtop) for STREAM s1
> fixit.pdb;
stream: opening fixit.pdb
Error: fixit.pdb: full pdb format not supported
Only ATOM records in amber order allowed
However, if I replace the pdb files with the original .restrt carnal
works.
My question is what is the way to do this calculation using .pdb files?
For the record, I am using amber7.
Thank you,
Ioana
Received on Thu Oct 31 2002 - 10:30:35 PST
