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
>
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Received on Mon May 24 2010 - 23:30:06 PDT
