Respected Sir,
Thank you for your reply.
Do you want to say energies after minimization? No I did not perform that
because I am not sure whether I am able to correctly combine the force
field and modifications and hence the reliability of the prmtop file. So
one my query is whether I can combine them like that or not??
Looking forward for your reply.
On Tue, Mar 22, 2016 at 4:59 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> do these give you different energies for the same structure?
>
> On Tue, Mar 22, 2016 at 2:25 AM, A kS <aks25121986.gmail.com> wrote:
>
> > Dear AMBER users,
> >
> > I want to *study the effect of phosphorylation of a serine residue on a
> > protein-DNA complex*.
> > I am willing to *use 99SBILDN for protein and bsc0 for DNA*.
> > I have also found the *parameter for phosphoserine* in:
> > http://sites.pharmacy.manchester.ac.uk/bryce/amber/
> >
> > Now to *check whether the combination of 99SBILDN+bsc0+Phosphoserine
> cause
> > any problem,* I have *generate the prmtop* file of *unmodified
> protein-DNA
> > complex in two ways*:
> >
> > **********************************
> > *1st*
> >
> > #Olnly 99SBILDNA+bsc0
> >
> > *source leaprc.ff99SBildn*
> >
> > *loadoff DNA_CI.lib*
> > *loadamberparams frcmod.parmbsc0*
> >
> > comp = loadpdb Prot-DNA.pdb
> >
> > addions comp Na+ 0
> > solvateOct comp TIP3PBOX 10.0
> >
> > check comp
> > saveamberparm comp *PD_inbox.prmtop* PD_inbox.inpcrd
> >
> >
> > *2nd*
> >
> > # 99SBILDN+bsc0+Phosphoserine
> >
> > source leaprc.ff99SBildn
> > loadoff DNA_CI.lib
> > loadamberparams frcmod.parmbsc0
> > *loadoff S2P.off*
> > *loadamberparams frcmod_s2p*
> >
> > comp = loadpdb Prot-DNA.pdb
> >
> > addions comp Na+ 0
> > solvateOct comp TIP3PBOX 10.0
> >
> > check comp
> > saveamberparm comp *PD_inbox_phos.prmtop* PD_inbox_phos.inpcrd
> >
> > ****************************************
> > *Problem:*
> >
> > 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*.
> > 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
> >
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Received on Tue Mar 22 2016 - 05:30:05 PDT
