From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Wed Jul 16 2014 - 12:53:47 CDT
The patch doesn't seem to have come through correctly; I see two RESI
entries in you e-mail, but no PRES.
There is no need to modify the topology entries for RESI ASP or RESI LYS;
all modification should be contained in the PRES entry. I'll be posting
another example later today or tomorrow.
As mentioned before, there exist standard charges for amide bonds in the
protein FF - no need to use any toolkits or imperfect analogies.
On 07/16/2014 02:27 AM, Sadegh Faramarzi Ganjabad wrote:
> 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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