From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Wed Jul 16 2014 - 01:27:52 CDT
Kenno
Followings are my residues and the patch; atoms connected by patch are
indicated by bold Italic letters.
As you said the sum of combined entity should be integer. However, in this
case amide residue is common between ASP and LYS. For example, if I
consider atom N as a part of amide residue, it won't be a part of LYS, and
LYS will lose an N atom and my new residue is LYS minus N. Then I have to
change partial charges on other atoms on LYS in order to make up losing
charge of N. Since this modification of partial charges seems to be
arbitrary, I'm using VMD Force Field Toolkit to reproduce partial charges
for all atoms.
Thanks
Sadegh
RESI ASP -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 OD1
ATOM HA HB1 0.09 ! | | / /
GROUP ! HA-CA--CB--*CG*
ATOM CB CT2A -0.28 ! | | \
ATOM HB1 HA2 0.09 ! | HB2 OD2(-)
ATOM HB2 HA2 0.09 ! O=C
ATOM CG CC 0.62 ! |
ATOM OD1 OC -0.76
ATOM OD2 OC -0.76
RESI LYS 0.00 ! modified to reflect cyclization,
GROUP ! nicotinamide parameters (3NAP cge
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1
ATOM HA HB1 0.09 ! | | | | | / |
GROUP ! HA-CA--CB--CG--CD--CE--* NZ*--HZ2
ATOM CB CT2 -0.18 ! | | | | | \ |
ATOM HB1 HA2 0.09 ! | HB2 HG2 HD2 HE2 HZ3
ATOM HB2 HA2 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.18 ! |
ATOM HG1 HA2 0.09 ! NC-HC1
ATOM HG2 HA2 0.09 ! |
GROUP ! HC2
ATOM CD CT2 -0.18
ATOM HD1 HA2 0.09
ATOM HD2 HA2 0.09
GROUP
ATOM CE CT2 0.21
ATOM HE1 HA2 0.05
ATOM HE2 HA2 0.05
ATOM NZ NH3 -0.30
ATOM HZ1 HC 0.33
ATOM HZ2 HC 0.33
ATOM HZ3 HC 0.33
GROUP
ATOM C CG2O1 0.630 ! 3NAP
ATOM O OG2D1 -0.460 ! 3NAP
ATOM NC NG2S2 -0.900 ! 3NAP
ATOM HC1 HGP1 0.390 ! 3NAP
ATOM HC2 HGP1 0.360 ! 3NAP
___________________________
PATCH;
1HB1 1HB2
\ /
--1CB
\
* 1CG*==OD1
\
*2NZ-* 2HZ1
|
2HE2 - 2CE- 2HE1
|
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