Hi Hemant,
It is not an error but warning, you should be able to proceed.
Basically when add solvation box, the program uses vdw radii to
detect contact, i.e. if the water atom is too close to your object,
the water
molecule will be excluded. By default it uses vdw radii from the amber
force field. If no AMBER force field was found, each atom will has radii
of 1.5 angstrom. NOTE the vdw radii is used only for solvation, the
generated
prmtop file will still have the correct vdw radii.
There is no way to fix this without changing the code. If you
like, I am
generate a patch for you which can fix this problem.
Sincerely,
Wei
On Mar 6, 2009, at 3:50 AM, Hemant Gangwar wrote:
>
> ---------------------------- Original Message
> ----------------------------
> Subject: Solvate Box od amoeba water
> From: "Hemant Gangwar" <hemant.physics.iisc.ernet.in>
> Date: Fri, March 6, 2009 3:00 pm
> To: amber.ambermd.org
> --------------------------------------------------------------------------
>
>
> I am using Amber10 . I am trying to Solvate Carbon nanotube(sp2
> carbons)in
> amoeba water using Sleap.I used following procedure
> Source leaprc.amoeba
> loadoff cnt.lib(lib file for CNT structure)
> solvatebox DEN WATBOX 4
> DEN is unit name for CNT & SP2 CARBON has been named as "CA" in
> cnt.lib file.
> I got following error message
>
> Warning: no amber force field has been loaded, VDW radii set to 1.5.
> Though leaprc.amoeba loads amoebapro.prm file.
> If I am trying to load other force field file than it says atom 202
> &203
> can not be identified.(atom 202 & 203 are amoeba water H &
> o ,defined in
> amoebapro.prm).
> thanks in advance.
>
>
> --
> Hemant Gangwar
> Graduate Student
> Centre for Condensed Matter Theory
> Indian Institute of Science
> Bangalore
> Mob-9632726167
> www.physics.iisc.ernet.in/~hemant
>
>
>
>
>
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Received on Sun Mar 08 2009 - 01:08:37 PST
