AMBER Archive (2004)

Subject: Re: AMBER: Angle parameters in phosphate groups

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Thu Aug 12 2004 - 09:18:06 CDT

Hi,

I'm only curious about this. What would happen if you just built
phosphoserine with N- and C-caps and run the same procedure you
gave? It's hard to tell where the problem is with what you gave in
your email.

Best,

Guanglei

Seongeun Yang wrote:
> Hi all,
>
> **********************************************************
> This is the second try to get your reply.
> Please take a look at this problem and give me a word.
> **********************************************************
>
> I'm doing md simulations of a small peptide in water and one of amino acids
> of the peptide is phosphoserine.
> The atomic partial charges of singly and doubly charged phosphoserines were
> calculated using antechamber.
> Both trajectories were run at 500 K using the parm99 parameters.
> But the problem is that the trajectory of the peptide having singly charged phosphoserine
> failed to run after a few picoseconds with vlimit exceeded while heated from 0 K to 500 K.
> Structures of the peptide were severely distorted and looked unreasonable.
> On the other hand, there was no problem in the case having doubly charged phosphoserine.
> Several other test simulations were done using a smaller time step, without using SHAKE for hydrogens, or by heating stepwisely, but still the trajectory failed with vlimit exceeded.
> So, I checked the parameters and found that the force constant for the angle O2-P-OH is
> only about half of the value in CHARMM.
>
> O2-P-OH 45.0 108.23 in Amber/parm99.dat
> O2-P-OH 98.9 108.23 in CHARMM/pardna_10_22.inp
> (ON3-P-ON4 98.9 108.23 in CHARMM/par_all27_prot_na.prm)
>
> In a new test simulation using the force constant larger than 45.0 for the angle O2-P-OH,
> for example 60.0, there was no problem in keeping the simulation running without vlimit exceeded.
>
> I'm wondering that the problem in simulating the peptide having singly charged phosphoserine
> lies in using the rather small force constant or in anything else.
> For reference, the input parameters used in heating the system are:
>
> &cntrl
> imin = 0, ntx = 1, irest = 0,
> ntpr = 500, ntave = 5000,
> ntwr = 500, iwrap = 0,
> ntwx = 0, ntwe = 0,
> ntf = 1, ntc = 2, ntb = 1,
> cut = 8.0, nsnb = 10,
> nstlim = 50000, dt = 0.002,
> tempi = 0.0, temp0 = 500.0,
> ntt = 1, tautp = 1.0
> &end
>
> Thanks for your attention and please give me some nice idea to get out of this problem.
>
> Seongeun Yang
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