AMBER Archive (2008)

Subject: Re: AMBER: problem with Dihedral angle potentials

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 30 2008 - 17:07:27 CDT

I suggest that you work through the tutorials for the non-standard
residue first.
There are many issues with what you propose, such as what other
parameters you will use with these, like the partial charges and vdw,
which also affect barrier heights. in principle you should use all of
the parameters that they proposed (all 3). hopefully going through the
tutorial will hep you see how to do that. mixing parameters from
different sources is pretty advanced, so you'll probably want to find
someone local that can walk you through it, or try the tutorials and
ask specific questions about the parts that you don't fully understand
or any error messages that you get.

On Thu, Oct 30, 2008 at 12:35 PM, aneesh cna <aneeshcna_at_gmail.com> wrote:
> Sorry for making you confused. I don't have much experience in MD.I want to
> use exact parameters from literature and trying to add these parameters in
> the frcmod file.For dihedral angle, in literature they mentioned three
> barrier height (Vn) values .These parameters are made for OPLS-AA
> framework.Out of these three barrier height values which one I wilI choose
> for mention in frcmod?.
>
> On Thu, Oct 30, 2008 at 10:20 AM, Carlos Simmerling
> <carlos.simmerling_at_gmail.com> wrote:
>>
>> I think it will be easier for us to help you if you give a lot more info.
>> are you trying to use exactly the parameters from the literature, or
>> develop your own similar to those?
>> are the ones you mentioned made for amber?
>> what is the specific question you mentioned that the tutorial does not
>> answer?
>> which tutorial did you try?
>> and finally, do you already have a lot of experience with MD?
>> developing your own parameters is very difficult unless you are
>> experienced with the basics already.
>>
>>
>>
>> On Thu, Oct 30, 2008 at 5:11 AM, aneesh cna <aneeshcna_at_gmail.com> wrote:
>> > Hello Carlos,
>> > Thanks for your reply.Sorry to say that in tutorials I
>> > couldn't able to found out the answer . Can u give me some more
>> > information
>> > ?
>> >
>> > Thanks in Advance
>> > Aneesh
>> >
>> > On Wed, Oct 29, 2008 at 3:39 PM, Carlos Simmerling
>> > <carlos.simmerling_at_gmail.com> wrote:
>> >>
>> >> have you looked at the tutorials?
>> >>
>> >>
>> >>
>> >> On Wed, Oct 29, 2008 at 5:23 AM, aneesh cna <aneeshcna_at_gmail.com>
>> >> wrote:
>> >> > Hello Amber Users,
>> >> > I am trying to generate 'frcmod' file for a
>> >> > molecule by looking at the literature. For barrier height, in
>> >> > literature
>> >> > they mentioned three values (V1,V2 and V3, i.e., triple cosine
>> >> > potential)
>> >> > and out of this V1 is positive and other two (V2 and V3) are
>> >> > negative.
>> >> > Which
>> >> > one should I choose to mention in Amber 'frcmod' file and How can I
>> >> > get
>> >> > the
>> >> > angle and periodicity corresponding to V1,V2 and V3 that is not
>> >> > there
>> >> > in
>> >> > literature?. I am using Amber 9.0 version.
>> >> >
>> >> > Thanks in Advance
>> >> > Aneesh
>> >> >
>> >> >
>> >> >
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