problem with ambpdb

From: Rozita Dara <rdara_at_uoguelph.ca>
Date: Sun 30 Sep 2001 12:16:24 -0400 (EDT)

Hi again,

I still have the old problem. As I mentioned before, I am running a very
simple minimization in water. I'm using the exact example on the tutorial.
When I run ambpdb to convert restrt file to pdb file, it produces lot of
unknown ATOM. When I run xleap to visualize this file I get this messages:

Unknown residue: B^^Y number: 6 type: Nonterminal
(Residue 7: .M-(M-U, Nonterminal, was not found in name map.)
Unknown residue: .M-(M-U number: 7 type: Nonterminal
(Residue 8: B C, Nonterminal, was not found in name map.)

Unknown residue: AM-.M-P number: 1988 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
(Residue 1989: A+M-R, Terminal/last, was not found in name map.)
Unknown residue: A+M-R number: 1989 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck

I don't know if there is a problem with my prmtop file or with leap.in
file. I am including my input files in the following. I would appreciate
any kinds of input. If it helps, I can send the prmtop file too.
  
Thanks for your time

Leap.in:

frcmod=loadamberparams frcmod.pcy
plc =loadpdb hmbp.H.pdb
addIons plc Cl- 0
solvateBox plc WATBOX216 10.0
saveAmberParm plc prmtop.wat prmcrd.wat

my input file (simple minimization)

min.in

&cntrl
  imin=1,
  ntc=2, ntb=1,
  maxcyc=1000, ntpr=100,
&end

OR if run molecular dynamics simulation. In both cases I have the same
problem.

md1.in

&cntrl
    imin=0, irest=0, ntx=1, tempi=0.,
    ntt=1, temp0=310.0, tautp=0.2,
    taup=0.2, ntp=1,
    ntf=2, ntc=2, ntb=2,
    nstlim=5,
    ntwe=2, ntwx=1, ntpr=1,
 &end
Received on Sun Sep 30 2001 - 09:16:24 PDT
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