But it seems weird just to leave two atoms... Maybe it wouldn‘t work... Hope others on the mailing list could help you.
________________________________
发件人: Huang ZiJian via AMBER <amber.ambermd.org>
发送时间: 2023年3月3日 13:45
收件人: angad sharma <angadsharma54.gmail.com>; AMBER Mailing List <amber.ambermd.org>
主题: [AMBER] 回复: Electrostatic Energy !
Hi,
1) One suggestion:
The way I could think of is use cpptraj to strip out all but the two atoms you want and generate corresponding topology and trajectory files. And use SANDER with imin=5 for post-processing, then get energy information in output file.
2)
I'm unfamiliar with CPPTRAJ 'energy' command. Maybe making the mask clear would help. Using ':1.OP2' or '.12' (Atom number) rather than just '.OP2'.
Hope this helps.
Best,
Zijian
________________________________
发件人: angad sharma via AMBER <amber.ambermd.org>
发送时间: 2023年3月2日 19:22
收件人: amber.ambermd.org <amber.ambermd.org>
主题: [AMBER] Electrostatic Energy !
Dear amber users,
I am calculating the electrostatic energy of OP1, OP2 and all the
electronegative atoms of the DNA.
Here are my input and output files for the calculation.
---------------------------------------------------------------------------------------------------------------------------------
*(1) input commands for OP2 of DNA(Considering all Electrostatic
interaction between Mg2+ and OP2)*
echo "" > op2-ene_nb.txt
for i in {1..5000}
do
echo "parm ../../dna-cu.prmtop
trajin ../../rdf-within5angs/auto-0.15M-mg2+-prod1000ns.nc $i $i
reference ../../rdf-within5angs/auto-0.15M-mg2+-prod1000ns.nc $i $i
energy nonb_el_vdw .OP2,MG out op2nonbond_frm.txt nonbond elec vdw
go
quit
" > cppt.in
cpptraj -i cppt.in
tail -n 1 op2nonbond_frm.txt >> op2-ene_nb.txt
done
*outputs are as the following for the above input command*
* 1 -0.1971 79499.5003 79499.3032 1
-0.2003 77473.7626 77473.5623 1 -0.1895
76910.5003 76910.3108 1 -0.1731
75851.1108 75850.9377 1 -0.1700 74233.7531
74233.5830*
*(2) input commands for OP2 of DNA(Considering all Electrostatic
interaction between Mg2+ and OP2 within 5 angstrom of DNA)*
echo "" > op2-ene_nb.txt
for i in {1..5000}
do
echo "parm ../../dna-cu.prmtop
trajin ../../rdf-within5angs/auto-0.15M-mg2+-prod1000ns.nc $i $i
reference ../../rdf-within5angs/auto-0.15M-mg2+-prod1000ns.nc $i $i
strip !(:1-24<:5.0) outprefix dna-mg-op2 nobox
energy nonb_el_vdw @OP2,MG out op2nonbond_frm.txt nonbond elec vdw
go
quit
" > cppt.in
cpptraj -i cppt.in
tail -n 1 op2nonbond_frm.txt >> op2-ene_nb.txt
done
*outputs are as the following for the above input command*
* 1 -0.2462 -1189.6295 -1189.8757 1
-0.2004 -880.8359 -881.0363 1 -0.2276
-1175.8230 -1176.0506 1 -0.1816
-1155.9435 -1156.1251 1 -0.2019 -1159.7541
-1159.9560*
*----------------------------------------------------------------------------------------------------------------*
IN the first case we are getting positive electrostatic energy because it
considers all the Mg2+ ions around DNA, so if it doesn't get OP2 then it
considers all the interactions between Mg2+ only.
In the second case i have confined the region, in this region we are
getting both opposite ions that's why it is negative.
For electronegative atoms all the Interaction of Mg2+ is coming positive.
So my question is what is the correct way to calculate the non bonded
electrostatic energy between two opposite charges, say one atom from DNA
and another Mg2+ from solvent.
*-------------------------------------------------*
*With Regards*
*Angad Sharma*
*Research Scholar*
*School of Computational & Integrative Sciences*
*Jawaharlal Nehru University*
*New Delhi 110067, (INDIA)*
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Received on Thu Mar 02 2023 - 22:30:02 PST
