Hi Jason,
Wow, I am glad you found my mistake early, before I produce more MD runs!
It works now with CYS changed to CYX following instructions in AmberTools manual. EGB in sander and pmemd matches.
I will *always* remember to check for disulfide bonds from now on!
Thank you so much,
Enghui
From: Jason Swails [jason.swails.gmail.com]
Sent: Tuesday, December 04, 2012 6:40 PM
To: AMBER Mailing List
Subject: Re: [AMBER] EGB discrepancy between sander and pmemd
You do have strongly overlapping atoms, which is a (fortunate!!) byproduct
of a different mistake. You forgot to add two CYS-CYS disulfide bonds when
you built your topology file. By leaving the residue named CYS (instead of
CYX), tleap automatically added hydrogens on the S atoms that were supposed
to be bonded to each other. These two hydrogens overlap strongly, and it's
these interactions that blew up your system.
This is something important to think about every time you go to create a
topology file of a protein. You have to make sure before-hand that not
only are the CYS residues involved in a disulfide bond renamed to CYX, but
that the necessary bond is formed. Loading a Amber prmtop into VMD will
display these bonds and help you diagnose this problem. I have been burned
by this enough myself (and had to throw away large amounts of useless MD),
which is why I'm so vigilant about it now.
Once you rebuild your topology file with the necessary disulfide bonds,
your errors should go away.
Good luck,
Jason
On Tue, Dec 4, 2012 at 6:29 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Tue, Dec 4, 2012 at 6:02 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Tue, Dec 04, 2012, Eng H Yap wrote:
>> >
>> > I am still trying to set igb=0 as suggested by Dave, but it seems then
>> > I'll need ntb=1, and I'll have to solvate the box in leap. Is that
>> > right?
>>
>> Sorry: easier path is to set igb=6, which turns off GB, but doesn't
>> require
>> (or allow) ntb=1.
>>
>
> I'll see if your results are reproducible with my version...
>
> pmemd actually prohibits all vacuum calculations -- there's a check
> against igb==0 with ntb==0 and igb==6. igb==0 with ntb==0 and igb==6 are
> sander-only options.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Dec 05 2012 - 09:00:02 PST
