AMBER Archive (2002)

Subject: NATOM mismatch in coord and topology files.

From: Narang Manpreet Kaur (preetdbs_at_iitr.ernet.in)
Date: Mon Nov 18 2002 - 00:49:46 CST

DBear amber users,
                   I have run minimization and dynamics of my drug
molecule in vacuum and while doing production dynamics the output fle for
production dynamics gives the following errors.

  FATAL: NATOM mismatch in coord and topology files.
But my initial coordinate file and coordinate files after minimization
and dynamics contains 58 atoms.
 
My input file is

 &cntrl
imin=0, temp0=300, tempi=300, dielc=1.0,ntt=1, cut=5, nmropt=0,
nscm=1000,igb=3,ntb=0,,ntf=1,ntx=5,irest=0, nstlim=10000,
vlimit=20,ntwv=100,ntwx=1000, ntwe=1000
 &end
-------------------------------------------------------------------------------The
The output file contains information regarding the no.of atoms as
 NATOM = 46 NTYPES = 8 NBONH = 22 MBONA = 26
 NTHETH = 48 MTHETA = 36 NPHIH = 76 MPHIA = 64
 HPARM = 0 NPARM = 0 NNB = 243 NRES = 1 NBONA = 26
 NTHETA = 36 NPHIA = 64 NUMBND = 11
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
I am not able to understand why 46 atoms ae read instead of 58.
While runnning the program it says
-p command not found.
/- Permission denied.
---------------------------------------------------------------------------
Please help. Thanks in advance.
Manpreet Kaur Narang
Research Scholar
Deptt.Biotechnology
Indian Institute of Technology
 Roorkee (IITR)
Roorkee, 247 667 India