On Thu, Dec 15, 2011, Jio M wrote:
>
> So I just tried to loadpdb TP3.pdb having only one water (file attached
> containing one water molecule; TP3.pdb) as follows
>
> loadamberparams parm99.dat
> loadoff solvents.lib
> WAT = copy TP3
>
> p = loadpdb TP3.pdb
>
>
> I get this error
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-H1-O-*
This is not an error, just an informational message that you can ignore: TIP3P
water (as implemented in Amber) has a non-physical H-H bond, used to keep the
molecule rigid. You can still do commands like "desc p", etc. and continue
with your work.
> source solvents.cmd
> xleap/tleap quits so I cannot loadpdb
As the message you get indicate, you can only run solvents.cmd when you are
inside the $AMBERHOME/dat/leap/lib directory. The purpose of the solvents.cmd
file is to create solvents.lib. Since you already have that, there is no need
to run solvents.cmd -- it's mainly there for developers, or for users who
might want to modify or extend solvents.lib.
....good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 16 2011 - 05:30:03 PST
