Dear Amber users,
I am new to Amber. I need to run MD simulations for a phosphorylated
protein kinase. I have created a INPCRD and PRMTOP files for my protein.
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.
Therefore I move on to minimisation by using the input files below.
*Min1.in (minimisation for solvent + ions)*
Imin=1,maxcyc=5000,ncyc=4900,
Ntb=1, ntr=1, ntc1,
Ntf=1, ntpr=100, cut=16
/
Hold protein fixed with a force constant of 500 kcal mol-1 angstrom-2
500.0
RES 1 301
END
END
*Min2.in (minimisation for protein + solvent + ions)*
Imin=1,maxcyc=5000,ncyc=4900,
Ntb=1, ntr=0, ntc1,
Ntf=1, ntpr=100, cut=16
/
After the run, I saw “RESTARTED DUE TO LINMIN FAILURE” towards the end of
the minimisation step (at NSTEP4900). I also noticed that I have a high
ENERGY, RMS and GMAX values
For example in step 4900
NSTEP ENERGY RMS GMAX NAME NUMBER
4900 3.4999E+07 2.1651E+11 5.3518E+13 O 2885
BOND = 1341.5027 ANGLE = 1831.3790 DIHED =
2992.2896
VDWAALS = 34058305.4132 EEL = -152044.9946 HBOND = 0.000
1-4 VDW = 1074043.6378 1-4 EEL = 12753.9772 RESTRAINT = 1.0033
EAMBER = 34999223.2048
These figures don’t seem right to me. But when I run overlapcheck in PTRAJ,
the atoms don’t seem to be overlapped with each other. When I move further
to heat minimisation, the TEMP appears to be NaN.
Does anyone has any ideas what’s going wrong to my model? Or what shall I
do in order to move on?
Your advice/suggestion is greatly appreciated.
Thank you
Best regards,
T
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Received on Mon Feb 18 2013 - 20:00:02 PST
