Thank you so much for the prompt reply. I have tried on the
non-phosphorylated protein, it works fine without error. So in this case, I
suspect is the problem of the phosphorylated residues only.
I created the input file of checkoverlap ptraj as below:
trajin [protein]
strip: WAT
strip: Na+
checkoverlap
The outcome did show up with few bad overlap, but when I check with the 3D
structure, the overlap doesn't seem like a big problem to me.
OVERLAP: atoms 2687 (:169.HB2) and 2695 (:170.H) are too close (0.877)!
OVERLAP: atoms 2832 (:179.CG) and 2864 (:181.HD3) are too close (0.771)!
OVERLAP: atoms 2833 (:179.HG) and 2862 (:181.CD) are too close (0.663)!
OVERLAP: atoms 2833 (:179.HG) and 2864 (:181.HD3) are too close (0.503)!
OVERLAP: atoms 2851 (:180.HG1) and 2885 (:182.O) are too close (0.182)!
OVERLAP: atoms 2859 (:180.C) and 2873 (:181.C) are too close (0.923)!
OVERLAP: atoms 2860 (:180.O) and 2874 (:181.O) are too close (0.573)!
OVERLAP: atoms 3708 (:238.HA) and 3727 (:238.C) are too close (0.585)!
OVERLAP: atoms 3739 (:240.HA) and 3749 (:240.C) are too close (0.557)!
OVERLAP: atoms 4700 (:300.O) and 4701 (:300.OXT) are too close (0.804)!
If really the bad overlap is the case that destroy the whole simulation
process, what sort of tools I can use to edit the bad contact?
Thank you for the advice. I will try to reduce the parameters as to what
you have suggested.
Regards,
T
On Tue, Feb 19, 2013 at 11:15 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Feb 19, 2013, Theodosia Teo wrote:
> >
> >
> > My protein kinase involves two phosphorylated residue. As I have no ideas
> > how to allow leap to recognise the force field of two phosphorylated
> > residues, I downloaded both OFF and FRCMOD files from
> > http://www.pharmacy.manchester.ac.uk/bryce/amber. I manually edited the
> > corresponding atom names of the residues so that they match the atom name
> > in OFF file. Everything runs well and I managed to generate the INPCRD
> and
> > PRMTOP files.
>
> This sounds fine, but a good debugging strategy would be to see if you
> encounter similar problems with the non-phosphorylated (standard) amino
> acids.
> That would help determine if the problem is with the protein structure you
> are
> using (you don't say what it is) or with the phorphorylation.
>
> > Hold protein fixed with a force constant of 500 kcal mol-1 angstrom-2
> > 500.0
>
> Consider reducing the restraint to 10.
>
>
> > *Min2.in (minimisation for protein + solvent + ions)*
> > Imin=1,maxcyc=5000,ncyc=4900,
> > Ntb=1, ntr=0, ntc1,
> > Ntf=1, ntpr=100, cut=16
>
> Set cut to 8 (the default), ntpr=1 (so you can see details of what is going
> on), maxcyc to 100.
>
> > VDWAALS = 34058305.4132 EEL = -152044.9946 HBOND = 0.000
>
> It is indeed very odd that you have a gigantic van der Waals term, yet
> ptraj
> reports no bad overlaps. It is so odd that might best initial advice is to
> double-check that you are interpreting the ptraj output correctly....sure
> it
> reports *some* bad overlaps(?)
>
> ....dac
>
>
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Received on Tue Feb 19 2013 - 14:00:02 PST
