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 Mon Mar 21 2016 - 23:30:05 PDT
