I tried to mimic the ras-raf example under
$AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots
using a different protein-protein complex but I keep
getting the error:
=>> Creating coordinates
Executing makecrd
Box info found: 88.562 84.776 76.124
Something wrong with NGR 3351 3350
Broken pipe
The box info corresponds to the box dimensions at the
end of the first trajectory in the trajectory file.
3350 is the last atom of the receptor protein
3351 is the first atom of the ligand protein
I can't seem to figure out why this does not work. I've
tried removing the lines with the box dimensions and
setting BOX option to "NO" but still get the same NGR
message.
Can someone tell me what I could be doing wrong?
Thank you,
Mark
=======================================================
My mm_pbsa.in file contains the section below:
----------------------------
.MAKECRD
BOX YES
NTOTAL 47678
NSTART 1
NSTOP 5
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 3351
LSTOP 5311
NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 1603
RSTART 1604
RSTOP 3350
----------------------------
I've checked the numbers and numbering of the atoms and
they seem correct.
The protein-protein complex was initially solvated with Cl-
ions and TIP3 (WATBOX216) in xleap.
It was mininization and dynamics were done with sander
using the input files below:
----------------------------
minimization run
&cntrl
imin=1,
maxcyc=100,
ntpr=20,
ntr=1,
&end
Restrain all atoms
10
RESIDUE 1 14477
END
END
----------------------------
molecular dynamics run
&cntrl
imin=0, irest=0,
ntx=1,
tempi=0.0, temp0=300.0,
ntt=1, tautp=0.2,
ntp=2, taup=0.2,
ntb=2, ntc=2, ntf=2,
nstlim=100,
ntwe=20, ntwx=20, ntpr=20,
&end
----------------------------
Received on Wed Apr 17 2002 - 14:52:41 PDT
