Re: Dihedral parameters for side-chains?

From: Igor Petrik (petrikigor_at_gmail.com)
Date: Mon Apr 26 2010 - 07:54:41 CDT

Jerome,

Thanks, I guess I will take a look at those, just to see how they match up.

I have another question now; I am trying to validate the bond and bend
parameters using the procedure given in the CGenFF tutorial (
http://mackerell.umaryland.edu/CHARMM_ff_params.html#CGenFF ;
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/tutorial.tgz)
and in the respective publication (
http://dx.doi.org/10.1002/jcc.21367 ), and I am stuck. It seems they use
CHARMM to calculate vibrational frequencies of the molecule and compare
those to "target" frequencies calculated by QM. I was able to calculate the
QM frequencies, but I am at a loss for how to calculate MM frequencies using
the "guessed" CHARMM parameters without CHARMM. Is there any program besides
CHARMM that will calculate vibrational frequencies using a set of CHARMM
input parameters? I don't think NAMD can do this can it?

Thanks,
- Igor Petrik
University of Illinois, School of Chemical Sciences
Department of Chemistry
CLSL A325, Box 74-5
600 S Mathews
Urbana, IL 61801

On Mon, Apr 26, 2010 at 07:29, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:

> Hi Igor,
>
> Nothing prevents you from doing *better* than CHARMM (no sarcasm at all,
> in case you wonder). If you are going to be fitting other dihedrals (and get
> the hang of the software toolchain), you might as well have a look at this
> one, at least to see how far off you are using the default CHARMM
> parameters. This is a fairly personal view, though, many people will tell
> you to just go ahead and stick with the default stuff.
>
> Jerome
>
>
>
> 2010/4/25 Igor Petrik <petrikigor_at_gmail.com>
>
> Jun,
>>
>> Ok, this is the one that I found... does that mean that I am not supposed
>> to parametrize that dihedral? Is it just supposed to be taken care of by
>> 1-4s in the CHARMM FF?
>>
>>
>> - Igor Petrik
>> University of Illinois, School of Chemical Sciences
>> Department of Chemistry
>> CLSL A325, Box 74-5
>> 600 S Mathews
>> Urbana, IL 61801
>>
>>
>> On Sat, Apr 24, 2010 at 22:29, Jun Zhang <coolrainbow_at_yahoo.cn> wrote:
>>
>>> Hi Igor :
>>>
>>> There is one line(2139) in the file:
>>>
>>> X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI
>>> ! alkane update, adm jr., 3/2/92
>>>
>>> Do you think it is what you need?
>>>
>>>
>>> Jun Zhang
>>> Nankai University
>>> coolrainbow_at_yahoo.cn
>>>
>>>
>>>
>

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