Replay to Parametrizing a novel residue]

From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Fri Sep 18 2009 - 13:58:11 CDT

Darja,

If you use MOPAC, try with PM6 and RM1 methods (MOPAC2009, for free
from http://openmopac.net/, portable with Vega), inclusion of solvent is
not so bad idea (keywords: EPS=78.4 NSPA=92 this is H2O implicit by
COSMO method). Better, if you have Gaussian try single point on MOPAC
optimized structures with large basis B3LYP/6-311G**; at ~ end of output
you can find Atomic charges with hydrogens summed into heavy atoms; also
you should find frequencies in output.
Hope this could be helpful
Sincerely

Branko

-------- Original Message --------
Subject: namd-l: Parametrizing a novel residue
Date: Fri, 18 Sep 2009 19:25:18 +0400
From: Дарья Шалаева <skorovesna_at_inbox.ru>
Reply-To: Дарья Шалаева <skorovesna_at_inbox.ru>
To: namd-l_at_ks.uiuc.edu

Dear NAMD users,

I am trying to make a topology of a new residue - ALA covalently bound
to SER-Ogamma by an amid bond (to study acil transfer reactions).
As I understood from the manual I need to specify the following things.

in topology
1/ charges for all atoms - by a float number
2/ single and double bonds - by specifying pairs of atoms
3/ impropers - by specifying 4 atoms to have an improper for

in parameter file
4/ parameters for all new bonds - equilibrium length and spring constant

I found several methods to calculate the charges (see below). I tested
them on a serine residue and got the following results:
> RESI SER 0.00
> ! genuine! VEGA ZZ ! !
> ATOM ! CHARMM ! Ammp-Mom Gasteiger ! MOPAC ! GAMESS+RESP (ESP-A1)
> ATOM N NH1 -0.47 -0.64 -0.03 0.08 -0.72
> ATOM HN H 0.31 0.34 0.28 0.76 0.48
> ATOM CA CT1 0.07 0.07 0.23 -0.29 -0.29
> ATOM HA HB 0.09 0.18 0.07 0.16 0.18
> ATOM CB CT2 0.05 0.05 0.08 0.08 0.31
> ATOM HB1 HA 0.09 0.18 0.06 0.04 0.04
> ATOM HB2 HA 0.09 0.17 0.06 0.10 0.04
> ATOM OG OH1 -0.66 -0.61 -0.39 -0.23 -0.66
> ATOM HG1 H 0.43 0.40 0.21 0.24 0.40
> ATOM C C 0.51 0.25 0.30 0.34 0.84
> ATOM O O -0.51 -0.40 -0.26 -0.25 -0.55
>
> Structure
>
> H O H H O H
> | || | | || |
> H-C-C------N--CA-C-------O-C-H
> | | |
> H HB1-CB-HB2 H
> |
> OG
> |
> HG1
>
It could be seen that all methods have a deviation from the genuine
CHARMM force field with Ammp-Mom method showing the best performance.
MOPAC and GAMESS+RESP constantly show negative charge on CA atom.
The next problem that I have spotted is that in CHARMM all atoms are
grouped (GROUP) to have a local zero charge. Unfortunately this is not
possible if using calculated values.

So, my first question is - which method should use and should I try to
make a local groups of zero charge by correcting a little bit the
calculated values?

My second question is - if I have to specify impropers as
IMPR N -C CA HN C CA +N O
IMPR NL CL CLA HLN1 CL CLA NL OL
IMPR CL OG OL CLA
how does the program knows how exactly to restrain the angle?

And my third question is how to calculate bond parameters? I`ve found
the way to calculate it using VEGA, but the manual says that the results
could be rough.

Thank you in advance.
da_shal


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