AMBER Archive (2005)

Subject: Re: AMBER: Can we load prmtop and inpcrd files into xleap?

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Wed May 18 2005 - 23:10:36 CDT

I guess I never thought of that. Good question. I created .lib files
for some of my portions that I had to change types/add charges so I can
just loadoff X.lib and it's now there so when I load my pdb, it knows
that portion already. Maybe this can help you.

Kara

On May 18, 2005, at 9:00 PM, Ilyas Yildirim wrote:

> Thats true; xleap is to create the prmtop/inpcrd files. But sometimes,
> I
> wanna do some changes on the structure (like changeing the
> type/charge).
> In that case, I have to follow every step again; create the .pdb file,
> load it into xleap, play with the types/charges/etc... If it is
> possible
> to load everything from .prmtop and .inpcrd file into xleap, I can
> easily
> change whatever I want to.
>
> On Wed, 18 May 2005, Kara Di Giorgio wrote:
>
>> I thought the main use for xLEaP was to CREATE prmtop and inpcrd
>> files
>> for other parts of amber (ie sander). Maybe I'm mistaken, though.
>>
>> Kara Di Giorgio
>>
>> On May 18, 2005, at 7:16 PM, Ilyas Yildirim wrote:
>>
>>> Hi all,
>>>
>>> If we have a .prmtop and .inpcrd file, we can create a .pdb file
>>> using
>>> ambpdb. And after getting the .pdb file, we can load it into xleap
>>> with
>>> 'loadpdb' command. I was wondering if we can load any .prmtop and
>>> .inpcrd
>>> files into xleap directly? The .prmtop file has all the atom
>>> type/charge/perturbation/etc... informations in it, and that will be
>>> pretty fast to load all these info into xleap. Thanks in advance.
>>>
>>> Best,
>>>
>>> --
>>> Ilyas Yildirim
>>> ---------------------------------------------------------------
>>> - Department of Chemisty - -
>>> - University of Rochester - -
>>> - Hutchison Hall, # B10 - -
>>> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
>>> - http://www.pas.rochester.edu/~yildirim/ -
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>>>
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>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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