[AMBER] disulfide bonds braking during MD simulation

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Mon, 30 Oct 2017 12:23:00 +0000

Dear Amber experts,

Many thanks to all of you who sent me
comments and advises on my problem reports about
errors in the MD simulation of protein containing non-standard
deprotonated Ser residue (SEM) and disulphide bonds.
I have finally resolved all problems and now MD is running correctly.
Below is the final correct variant of the input file for tleap.

source leaprc.protein.ff14SB
source leaprc.water.tip3p
loadAmberPrep SEM.prepin
loadAmberParams frcmod2.SEM
loadAmberParams frcmod1.SEM
mc = loadPDB 1fle_mod_opt_sem_nh.pdb
bond mc.31.SG mc.47.SG
bond mc.128.SG mc.195.SG
bond mc.159.SG mc.175.SG
bond mc.185.SG mc.215.SG
bond mc.248.SG mc.277.SG
bond mc.255.SG mc.281.SG
bond mc.264.SG mc.276.SG
bond mc.270.SG mc.285.SG
addions2 mc Cl- 0
solvateoct mc TIP3PBOX 15
saveamberparm mc mc.prmtop mc.inpcrd

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Received on Mon Oct 30 2017 - 05:30:04 PDT
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