[AMBER] cholorform solvent very high energy

From: Fabian Glaser via AMBER <amber.ambermd.org>
Date: Wed, 22 Jun 2022 14:12:39 +0300

Dear experts,

I am working for a while with a peptide like molecule, simulating it with different conditions and with water and methanol solvents, works perfectly well. But when I used chloroform solvent with exactly the same conditions, the runs start but fails very after 1ns or so because of energy shooting up.

The pdb looks OK, everything looks normal when it starts, I also tried to run sander for minimization and it worked better, the energy was lower, but when I start the dynamics with pmemd.cuda or pmemd it shoots up again.

I don’t know where to look for the problem, I would appreciate very much any help. Below is the tleap file I am using, which is exactly the same as for methanol or water excepting the box command.

Thansk a lot,

source leaprc.protein.ff19SB
source leaprc.gaff2

loadamberparams frcmod.opc3
loadamberparams frcmod.meoh
loadamberparams frcmod.chcl3

set default PBradii mbondi3

loadamberparams frcmod.ions234lm_1264_tip3p

loadamberparams 6AQ.frcmod
loadamberparams 7HC.frcmod
loadamberparams connect.frcmod
loadoff 6AQ.libx
loadoff 7HC.libx

COM = loadpdb peptide_ext_min.pdb

savepdb COM Ax8_ext.chcl3.dry.pdb
saveamberparm COM Ax8_ext.chcl3.dry.prmtop Ax8_ext.chcl3.dry.rst7

solvateoct COM CHCL3BOX 15

#addions COM Na+ 0
#addions COM Cl- 0

savepdb COM Ax8_ext.chcl3.solv.pdb
saveamberparm COM Ax8_ext.chcl3.solv.prmtop Ax8_ext.chcl3.solv.rst7


Fabian Glaser, PhD

Structural and Computational Biology Unit
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel

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Received on Thu Aug 04 2022 - 13:33:05 PDT
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