AMBER Archive (2005)

Subject: Re: AMBER: rotating and repositioning molecules in xleap

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Sun May 22 2005 - 08:03:40 CDT

Thanks for your reply, but I still have a question.
I knew that I can rotate molecules in the edit window, but it does not
modify coordinates of molecules. I mean that I can visually rotate
molecules in edit window, but when I close the edit, they still have
original coordinates. I know that I can set up center of box in xleap,
but I don't know how to modify coordinates by rotating molecules
conveniently in xleap.
Thanks for your help in advance.

best,
Hwankyu.

On May 22, 2005, at 5:37 AM, Angelo Pugliese wrote:

> In the Edit window of Xleap there are all the commands that you
> need....just play around with it.
>
> When you connect two molecule they become one single entity ( one
> molecule) so you need to add parameters for this new molecule....the
> easiest thing is to find the new parameters by analogy with other
> parameters already in the AMBER database and upgrade your .frcmod file.
>
> Hope it helps
>
> Angelo
>
>
>
> Hwankyu Lee wrote:
>
>> Dear Amber-users,
>>
>> 1) I'm connecting two molecules in xleap, and want to position those
>> molecules with specific configuration. I thought I can do that in edit
>> of xleap, but cannot find how to do this. Could you tell me how to
>> rotate and reposition molecules in xleap ? Is it possible in edit
>> (visual tool) of xleap?
>>
>> 2) Although I had .frcmod file by using parmchk, when I connected two
>> molecules, I got an error like "could not find angle parameter" or
>> "Could not find bond~~". In that case, how can I get reasonable
>> angle,
>> bond or torsion parameters?
>>
>> Thanks for your help in advance.
>>
>> best,
>> Hwankyu.
>>
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