[AMBER] disulfide bonds braking during MD simulation

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Tue, 24 Oct 2017 14:59:52 +0000

Dear Amber experts,

I have observed braking of disulfide bonds between CYX residues

in protein during MD simulation by Amber16.

I used ff14SB force field.

During protein preparing I have defined in tleap input script file all CYX

pairs connected by disulfide bonds (see below).

I would appreciate your advice how to resolve the problem.

Thank you,


Script for tleap:

source leaprc.protein.ff14SB
source leaprc.water.tip3p
mc = loadPDB 1fle_nh.pdb
bond mc.31.SG mc.47.SG
bond mc.128.SG mc.195.SG
bond mc.159.SG prot.175.SG
bond mc.185.SG mc.215.SG
bond mc.248.SG mc.277.SG
bond mc.255.SG prot.281.SG
bond mc.264.SG mc.276.SG
bond mc.270.SG prot.285.SG
addions2 mc Cl- 0
solvateoct mc TIP3PBOX 15
saveamberparm mc mc.prmtop mc.inpcrd

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Received on Tue Oct 24 2017 - 08:30:03 PDT
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