AMBER Archive (2006)

Subject: Re: AMBER: force field parameters

From: Navnit Kumar Mishra (navnit_at_chemi.muni.cz)
Date: Fri May 19 2006 - 06:01:59 CDT

Sorry, I couldn't get it properly before, you are right.
You can try Glycame force field parameter and force field for your
nonplaner part of atom, This is only my suggestion may be it will be
helpful.

Navnit

Douali, Latifa wrote:

> Thank you for reply. But in my understanding is that CM is an sp2
>carbon
>
>Latifa
>
>
>
>
>Hello Douali;
>
>I think the problem is with defining CM, because in png file I can see
>the methyl carbon as CT . You can change your atom type as CM.
>
>
>It will work.
>
>Good luck,
>
>Navnit
>
>
>Douali, Latifa wrote:
>
>
>
>>Dear AMBER users,
>>
>>I am running an MD simulation for a non standard nucleic acid which is
>>non planar.
>>In this structure, I have a methyl group in a pseudo axial position.
>>My question is:
>>1) how can I prevent this methyl from inverting to the equatorial
>>position.
>>The improper dihedrals I used for these simulations are as follow:
>>
>>CT-C-N*-CT 1.1 180.0 2.0
>>CT-C-N*-CM 1.1 180.0 2.0
>>C-CT-CT-CT 1.1 180.0 2.0
>>N*-OH-CT-HC 1.1 180.0 2.0
>>CT-OH-CT-HC 1.1 180.0 2.0
>>N*-CT-CT-HC 1.1 180.0 2.0
>>
>>2) May the proper dihedral angles also play a role in this transition
>>Attached is the structure of this system with the atom types assigned.
>>
>>
>I
>
>
>>might be doing something wrong,
>>any advice will be welcome
>>
>>
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