AMBER Archive (2006)

Subject: Re: AMBER: SHAKE problem after minimization

From: Rachel (comeonsos_at_googlemail.com)
Date: Wed Nov 22 2006 - 13:37:15 CST

Dear Hayden,

Thanks for your reply, yes, i do have some home-made residues, which are
hydrogen molecules, i used a three-atom model, with two hydrogen atoms (type
HD) and one dummy atom in-between the two hydrogen atoms (type DH), and the
charge of both HD are -0.475, and +0.95 on DH, and the following is the
.frcmod file i used for this residue:
######################################
# H2 molecule parameters

MASS
HD 1.008
DH 1.008

BOND
HD-DH 150.00 0.742
HD-HD 150.0 1.484

ANGLE
HD-DH-HD 500.0 180.0
HD-HD-DH 0.000 180.0

DIHEDRAL

IMPROPER
NONBON
HD 0.000 0.000
DH 2.920 0.2722
#########################################

As you can seen, I assumed the mass of DH is the same as HD (which is not
correct). And as i wanted to keep these three atoms in the same line, so i
added one extra bond between two HD atoms as suggested by Yong. So shall i
increase the force constant for HD-DH-HD or HD-HD-DH or both?

Thanks very much!
Best regards,
Rachel

On 11/22/06, Hayden Eastwood <s0237717_at_sms.ed.ac.uk> wrote:
>
> Dear Rachel
>
> I have had similar problems to you when running dynamics with home-made
> residues. There is a defect in the amber force field with regards to
> treating various highly charged groups in bonding proximity. If you have a
> home made molecule then I have the following question:
>
> Do you have any Phosphate-oxygen bonding neighbours with very large
> opposite
> charges? Or any other bonding pairs with huge charge differences? If you
> do,
> this could be the cause of the crash. AMBER assumes that the bond angle
> barrier is large enough to prevent neighbouring connected atoms from
> collapsing into one another. However, in some situations (i.e. with
> oppositely highly-charged atom pairs) this barrier is overcome and the
> atoms
> are pulled down a pairwise electrostatic interaction slope until they
> overlap and cause your energy to go crazy.
>
> The cure: artificially increase the bond angle force constants in the
> force
> field parameter file and this should prevent them running into each other
> (although the dynamical behaviour of some of the affected groups will of
> course be "stiffer").
>
> I don't really understand the nuts and bolts of why the atoms descend into
> one another given that there should be van der waals terms that prevent
> this...Mike Crowley personally explained it to me once and whilst it made
> sense at the time the explanation now seems a little fuzzy!
>
> If it's not a home made residue with the above mentioned characteristics
> then I'd suggest you follow Ross's advice.
>
> Best
>
> Hayden
>
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