I tried using the prepin file of Nadp+ -3 charged and netralised the system in
tleap by addions command, it worked properly. Thanks to all for help and
suggestions.
With regards,
Nicee.
> Thank you for the reply and suggestion. I have one more query. The prepin file
I
> have used for Nadp is the one I have generated from antechamber. I am feeling
that there is some problem with the parameters in it so I thought of using the
one in the amber parameter database. But it has parameters of nadp+ with -3
and
> -2 charge. Can i use this file as such with my system or do I need to
neutralize
> the charge, if yes then how?
>
>
>> On Mon, May 24, 2010, Nicee wrote:
>>> I am trying to minimize a protein which has aspartate, po4, glycerol , Nadp
and water in pdb file. I have generated prepin and frcmod file for all of
the above from antechamber as per tutorial and loaded them in tleap and
saved the prmtop and inpcrd file, but on miminizing the protein for 500
steps the minimization stops at 230 step and gives the following error :
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 230 -2.2468E+04 1.2248E+04 9.9638E+05 O3P 5114
>>> BOND = 358.4270 ANGLE = 826.4138 DIHED =
3289.6600
>>> VDWAALS = -2513.4377 EEL = -25000.7354 HBOND = 0.0000
1-4 VDW = 1148.6144 1-4 EEL = -577.0991 RESTRAINT = 0.0000
Frac coord min, max: -0.338855902014186 1.12539885977885
>>> Frac coord min, max: -0.338855902014186 1.12539885977885 The system
has extended beyond
>>> the extent of the virtual box.
>>> ntb=0,
>>> cut=10
>> You are asking for a vacuum simulation of a highly polar system, which is
likely to have high forces and be unstable. My guess is that you will need
to solvate your system, and run it as a periodic system.
>>> I tried run a similar minimization with maxcyc=230 and the
>>> .out and .restrt file were generated. Then i generated pdb
>>> (new7_mtb3_min12_pdb.pdb) for this restrt file and visualized it in pdb. The
O3P and H22 atom appeared to be overlapped.
>> Problems like this are not uncommon for phosphate-containing systems. It is
possible (likely?) that the H22 atom has zero Lennard-Jones parameters, which
may need to be fixed.
>> ....dac
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 25 2010 - 00:30:04 PDT
