Yes I did use the bond command to link the SG atoms.
Thanks again,
Enghui
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Wednesday, December 05, 2012 1:12 PM
To: AMBER Mailing List
Subject: Re: [AMBER] FW: EGB discrepancy between sander and pmemd
On Wed, Dec 5, 2012 at 11:56 AM, Eng H Yap <eyap.einstein.yu.edu> wrote:
> 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.
>
Did you use the "bond" command in tleap and visualize in VMD to make sure
that the bond is physically present? Changing CYS->CYX is not enough
(unless you leave the CONECT records in the PDB file correctly).
Good luck!
Jason
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 13:00:02 PST
