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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--
-------------------------
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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Received on Tue Mar 22 2016 - 07:30:03 PDT
