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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Received on Tue Mar 22 2016 - 04:30:03 PDT
