Thank you Prof. Case.
*******************************
Mohd Farid Ismail
Graduate Teaching Assistant
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: case [case.biomaps.rutgers.edu]
Sent: Saturday, January 26, 2013 1:31 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Mixing Small Organic + Water
On Sat, Jan 26, 2013, Ismail, Mohd F. wrote:
> Hi, I want to simulate a small organic molecule with water. If I only
> do tleap -s -f leaprc.gaff, and load the pdb file containing the both
> molecules, then leap will not create prmtop and inpcrd file. The error
> is something like Amber could not find type HW.
This makes complete sense: leaprc.gaff does not load any information about
water. In fact, leaprc.gaff doesn't load anything about any molecules at all,
and just has force field parameters. You have to load a mol2 (or similar)
file to describe your organic molecule.
>
> So what I did was load leaprc.gaff, then the prep files for the small
> organics, and then I did loadamberparams parm10.dat, before I load the
> pdb file. Will the parameter for the small organic be from GAFF, or
> parm10 if I do it this way. If not, is there another way to create this
> mixture?
You need to source *both* leaprc.gaff and leaprc.ff10 (or similar), in order
to get the library files for water as well as the water parameters. As noted
above, you also have to load the mol2 file for the organic molecule. There
won't be any competition between the two: gaff atom types are all lower case,
and water (and other Amber) atoms types are all upper case. So you can have
both loaded at the same time.
Finally, if you ever have questions about exactly what is in the prmtop files
leap has created, you can use the ParmEd program (or the older rdparm program)
to print data out in nice format to check on what you have.
...good luck...dac
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Received on Sat Jan 26 2013 - 20:30:03 PST
