Hi Carlos,
Yes I have red the leap.log file.
Wat I see there regarding the CYX residues are lines like this one:
(Residue 194: CYX, Nonterminal, was not found in name map.)
Is it a report about an error?
Anyway, did you find an error in the input script for tleap
in my previous email?
I would appreciate a bit more detailed comment that would help
me to resolve the problem with disulfide bonds braking.
Thank you,
Michael
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Tuesday, October 24, 2017 6:07:21 PM
To: AMBER Mailing List
Subject: Re: [AMBER] disulfide bonds braking during MD simulation
Did you read the leap.log file?
On Oct 24, 2017 11:00 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
wrote:
> 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,
>
> Michael
>
>
> 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
> quit
>
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>
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Received on Tue Oct 24 2017 - 09:00:03 PDT
