Dear Carlos,
I have examined by VMD the generated by tleap the mc.prmtop and mc.inpcrd
files of my protein. The VMD version on my computer has the Amber7 Parm
option for the new molecule loading. The structure of the protein
generated by VMD was corrupted .
I have used another option by the Amber function:
ambpdb -p mc.prmtop < mc.inpcrd > mc_init.pdb
Now the protein structure was correct and all disulfide bonds were intact.
Your comment appreciated.
Michael
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Wednesday, October 25, 2017 9:44:55 PM
To: AMBER Mailing List
Subject: Re: [AMBER] disulfide bonds braking during MD simulation
No it is not the case that ff14SB does not work for disulfide bonds. There
is no problem with the force field for that. You should look carefully at
the leap.log file in the section where it is making the bonds and see what
messages you get. Does it find the residue/atom pairs you specify? Using
restraints will NOT give you the correct behavior since the atoms do not
have covalent structure that way (with correct angles and dihedrals, and
nonbonded exclusions).
Load your prmtop and inpcrd into a program like VMD and you should see the
disulfide bonds drawn. If not, you do not have the correct prmtop yet.
On Oct 25, 2017 2:38 PM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
wrote:
Dear David,
Thank you for your email.
Yes there were a typo error you have identified.
I have corrected it but some disulfide bonds were anyway
broken even by the first minimization.
I have decided to use the disulfide bonds restraints.
After some faults with the input file construction for the minimization
I got the correct result - all disulfide bonds remained intact.
Nevertheless, the principal question remains.
Could the reason of the broken disulfide bonds is a pitfall of the ff14SB
force field parametrization and therefore one needs to use
an artificial tool of the restraint bond distances in order to keep intact
disulfide bonds during minimization and MD simulations?
Thank you,
Michael
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, October 25, 2017 3:39:09 AM
To: AMBER Mailing List
Subject: Re: [AMBER] disulfide bonds braking during MD simulation
On Tue, Oct 24, 2017, Michael Shokhen wrote:
>
> I have observed braking of disulfide bonds between CYX residues
This implies that the bonds were never properly created.
>
>
> 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
^^^^ ???
What is "prot"? It doesn't seem to have been defined, and it would not
be surprising if the expected bond were breaking.
As Carlos pointed out, this problem is almost certainly noted in the tleap
output, and it's good to learn what to look for. Another good idea (TM)
is to use the "checkvalidity" command in parmed: it searches for missing
disulfide bonds.
But to developers: this points up two genuine problems with tleap:
1. The output is so voluminous that people understandably have a hard
time reading it.
2. tleap really should quit when errors like this are encounterd. I
understand that this would break some existing scripts, but the
benefits are likely to outweigh the disadvantages.
I suppose I should be the one to attack this, but it would be really great
if someone would step up to the plate (this being World Series time....)
It's really pretty trivial coding to find these and other error messages
and make them fatal. Removing un-needed messages is more of an art, but
is still super-straightforward.
...dac
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Received on Wed Oct 25 2017 - 13:00:02 PDT
