RE: Re:Subject: Re: Subject: Re:Re: New partial charges after patching

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Jul 16 2014 - 18:44:39 CDT

A suggestion: the patch would be much simpler (and the end result identical) if you first mutate your ASP residue to ASN. Delete NZ, HZ1, HZ2 and HZ3 off the lysine and one of the amide hydrogens off the ASN, bond the amide nitrogen to the lysine CE, and with some minor tinkering with atom types and charges, you’re essentially done.

I’ve pasted below a patch I put together some time back to do this between a glutamine and lysine residue. Somewhat rough-and-ready, but it behaves itself.

PRES ISOP 0.00000 ! gamma-glutamyl lysine isopeptide bond
GROUP
                            ! 2HE1 2HD1
                            ! | |
ATOM 1NE2 NH1 -0.48 ! 1HG1 1OE1 2CE-----2CD-----2CG
ATOM 1HE22 H 0.31 ! | || / | |
ATOM 2CE CT2 0.07 ! -1CG--1CD--1NE2 2HE2 2HD2
ATOM 2HE1 HA 0.05 ! | \
ATOM 2HE2 HA 0.05 ! 1HG2 1HE22

DELETE ATOM 1HE21
DELETE ATOM 2HZ1
DELETE ATOM 2HZ2
DELETE ATOM 2HZ3
DELETE ATOM 2NZ

BOND 1NE2 2CE
IMPR 1NE2 1CD 2CE 1HE22

From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Sadegh Faramarzi Ganjabad
Sent: Wednesday, 16 July 2014 4:28 PM
To: namd-l_at_ks.uiuc.edu
Subject: Re:Subject: Re: Subject: Re:Re: namd-l: New partial charges after patching

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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