Re: Replay to Parametrizing a novel residue]

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Fri Sep 18 2009 - 15:19:33 CDT

Hello,

I am working together with Dasha. Thank you for quick reply. The problem is
that MOPAC calculates the charges that differ to much from the original
force field. And this can badly affect the results of calculation. And
another question is has important are those GROUPs - that is groups of atoms
that have local zero charge. To me it sound obvious that this is an artifact
and this is most likely some FF workout.
Any comments on this and the other questions?

Thank you for your time.
SDA

2009/9/18 Branko <bdrakuli_at_chem.bg.ac.yu>

> 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> <skorovesna_at_inbox.ru> Reply-To: Дарья Шалаева
> <skorovesna_at_inbox.ru> <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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