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
