Thanks so much again, Dmitry.
That will really clear things up for me.
Have a great day.
Dean
PS. I still don't understand why such essential background material is not
in the most recent manuals. Most beginners would never assume that they
need to go to "old version" manuals for the basics. There would be so much
less confusion for new learners (who did not go through the history of the
development of the software like the developers) if it was all in the most
current version manual. Just my 2cents.
Dr. Dean Cuebas, Associate Professor of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: Dmitry Nilov <nilovdm.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Thu, 15 Apr 2010 07:42:21 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] How do you know when to include improper dihedrals????
>
> You could look at amber10/dat/leap/prep/all_amino94.inand
> amber10/dat/leap/prep/
> all_nuc94.in to learn how to use impropers in amino acids and nucleic
> acids. Also you could check p.261 of Amber 8(!) manual.
>
> On Mon, Apr 12, 2010 at 11:30 PM, Dean Cuebas
> <deancuebas.missouristate.edu>wrote:
>
>> Dear amberers,
>>
>> I guess my question is more to Ross Walker, since he is the one whose
>> parameterized NAD+ files I am referring to, but I'll accept a clarification
>> from anyone! :-)
>>
>> Using the .mol2 file with charges and amber atomtypes for NAD+ with parmchk
>> and the parm99.dat file, a frcmod file is created that contains improper
>> dihedrals for the aromatic adenine ring system. Yet, in the frcmod file
>> provided by Ross Walker, there are no such improper dihedrals specified.
>>
>> First let me say that I am not implying a mistake on Ross's part, because
>> I've seen a few other instances where this is the case also.
>>
>> So my question is, when are the impropers that are supplied in the frcmod
>> file produced by parmchk not necessary?
>>
>> For example, I have a compound I am parameterizing that contains planar
>> amides and planar thioester linkages. Using parmchk with the parm99.dat
>> file
>> gives me impropers in the frcmod file with for each of these, with a large
>> force constant of 10.5.
>>
>> Do I need these specifications for these planar linkages??
>> How do you decide???
>>
>> Thanks so very much for your help in advance.
>>
>> With regards,
>>
>> Dean
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Dmitry Nilov,
> Lomonosov Moscow State University
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Received on Thu Apr 15 2010 - 09:00:03 PDT
