AMBER Archive (2002)

Subject: carnal

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Oct 31 2002 - 12:30:35 CST

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