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 - 05:00:02 PST
