Respected Sir,
Thank you very much for your reply. Your reply is really helpful but at the
same time I am really afraid!!!!.
I was have an idea that if the PDB does not have residue name S2P LEaP will
not include the parameter of frcmod_s2p.
Now I am totally confused, it seems that I can not include frcmod of bsc0
with protein force field to simulate a protein DNA complex because DNA may
have some bonds that are common with protein and then those bond of
protein will also get modify. Moreover it seems very difficult to combine
modifications even if they are originated from same force field.
I am really clueless please help.
regards
On Tue, Mar 22, 2016 at 7:55 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Tue, Mar 22, 2016 at 12:25 AM, A kS <aks25121986.gmail.com> wrote:
> > In my opinion *since the Prot-DNA.pdb does not have any phosphoserine*
> the t*wo
> > prmtop PD_inbox.prmtop and PD_inbox_phos.prmtop will be same*.
>
> This is incorrect. LEaP assigns parameters based on atom types, not
> functional groups. Your parameter file 'frcmod_s2p' contains
> parameters for a bond with P-OS atom types, which your DNA does have
> (e.g. P-O5', P-O3'). Therefore when you load 'frcmod_s2p' you are
> modifying the parameters for these bonds.
>
> -Dan
>
> > However, *when I use command diff to check the difference between them* I
> > found that at *line number 40188 in both of the prmtop file there exists
> > difference in value of force constants* (marked in bold):
> >
> > *****************************************
> > *PD_inbox.prmtop*
> >
> > %FLAG BOND_FORCE_CONSTANT
> > %FORMAT(5E16.8)
> > 5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02
> > 3.40000000E+02
> > 3.10000000E+02 4.34000000E+02 3.37000000E+02 3.40000000E+02
> > 3.10000000E+02
> > 4.34000000E+02 3.40000000E+02 3.67000000E+02 4.34000000E+02
> > 4.81000000E+02
> > 3.37000000E+02 5.70000000E+02 4.90000000E+02 3.17000000E+02
> > 5.53000000E+02
> > 3.20000000E+02 6.56000000E+02 2.27000000E+02 6.56000000E+02
> > 3.17000000E+02
> > 3.67000000E+02 4.69000000E+02 4.50000000E+02 4.69000000E+02
> > 3.17000000E+02
> > 3.67000000E+02 4.34000000E+02 4.27000000E+02 3.67000000E+02
> > 4.77000000E+02
> > *4.88000000E+02 4.10000000E+02 5.18000000E+02 3.17000000E+02
> > 5.25000000E+02*
> > 3.20000000E+02 4.61000000E+02 4.83000000E+02 4.27000000E+02
> > 4.18000000E+02
> > 4.47000000E+02 5.20000000E+02 4.14000000E+02 3.67000000E+02
> > 5.29000000E+02
> > 4.40000000E+02 4.36000000E+02 3.40000000E+02 3.37000000E+02
> > 3.40000000E+02
> > 3.10000000E+02 3.20000000E+02 3.20000000E+02 5.25000000E+02
> > 3.67000000E+02
> > 5.02000000E+02 4.69000000E+02 3.17000000E+02 4.10000000E+02
> > 3.67000000E+02
> > 5.49000000E+02 4.48000000E+02 4.24000000E+02 4.57000000E+02
> > 3.67000000E+02
> > 4.27000000E+02 5.53000000E+02 5.53000000E+02
> >
> >
> >
> > *PD_inbox_phos.prmtop*
> >
> > %FLAG BOND_FORCE_CONSTANT
> > %FORMAT(5E16.8)
> > 5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02
> > 3.40000000E+02
> > 3.10000000E+02 4.34000000E+02 3.37000000E+02 3.40000000E+02
> > 3.10000000E+02
> > 4.34000000E+02 3.40000000E+02 3.67000000E+02 4.34000000E+02
> > 4.81000000E+02
> > 3.37000000E+02 5.70000000E+02 4.90000000E+02 3.17000000E+02
> > 5.53000000E+02
> > 3.20000000E+02 6.56000000E+02 2.27000000E+02 6.56000000E+02
> > 3.17000000E+02
> > 3.67000000E+02 4.69000000E+02 4.50000000E+02 4.69000000E+02
> > 3.17000000E+02
> > 3.67000000E+02 4.34000000E+02 4.27000000E+02 3.67000000E+02
> > 4.77000000E+02
> > *4.88000000E+02 4.10000000E+02 5.18000000E+02 3.17000000E+02
> > 2.30000000E+02*
> > 3.20000000E+02 4.61000000E+02 4.83000000E+02 4.27000000E+02
> > 4.18000000E+02
> > 4.47000000E+02 5.20000000E+02 4.14000000E+02 3.67000000E+02
> > 5.29000000E+02
> > 4.40000000E+02 4.36000000E+02 3.40000000E+02 3.37000000E+02
> > 3.40000000E+02
> > 3.10000000E+02 3.20000000E+02 3.20000000E+02 5.25000000E+02
> > 3.67000000E+02
> > 5.02000000E+02 4.69000000E+02 3.17000000E+02 4.10000000E+02
> > 3.67000000E+02
> > 5.49000000E+02 4.48000000E+02 4.24000000E+02 4.57000000E+02
> > 3.67000000E+02
> > 4.27000000E+02 5.53000000E+02 5.53000000E+02
> >
> >
> > ******************************************
> > I am unable to understand why this difference come?? Am I incorrectly
> > combining the force field and modifications??
> >
> > Looking forward for your reply
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 22 2016 - 23:30:02 PDT
