[AMBER] Breaking of complex molecule

From: richa anand <richaaanand.gmail.com>
Date: Wed, 23 Jun 2021 09:30:27 +0530

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


addions COMPLEX Cl- 1

solvateOct COMPLEX TIP3PBOX 12.00

charge COMPLEX

saveAmberParm COMPLEX complex.prm.top complex.prm.crd

savepdb COMPLEX complex_out.pdb


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,
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Received on Tue Jun 22 2021 - 21:30:02 PDT
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