Dear Users,
I am trying to simulate "protein-ligand complex", for which the Tleap input
parameters used are given below:
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadamberprep UNK_clean_H.prepi
loadamberparams UNK.frcmod
COMPLEX = loadpdb complex_clean_H.pdb
check COMPLEX
addions COMPLEX Cl- 1
solvateOct COMPLEX TIP3PBOX 12.00
charge COMPLEX
saveAmberParm COMPLEX complex.prm.top complex.prm.crd
savepdb COMPLEX complex_out.pdb
quit
but when I extracted the pdb file after minimization of 1000 steps, the
complex got broken. While, the energy seems ok. All parameters in energy
file is ok. Is this (breaking of molecule) the problem of improper force
field or water model.
For once I had faced the same problem with protein-RNA complex, but that
time I changed solvatBox to solvateOct and it worked. BUt, unfortunately
it's not working this time.
KIndly suggest me what to do?
Thanking You,
Richa
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Received on Tue Jun 22 2021 - 21:30:02 PDT
