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,
Fabian
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
quit
--------------------------
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:33:05 PDT
