AMBER Archive (2009)

Subject: Re: [AMBER] Solvate Box od amoeba water

From: Hemant Kumar (hemant_at_physics.iisc.ernet.in)
Date: Sun Mar 22 2009 - 11:06:01 CDT

Hi wei & amber user,
thanks for your suggestion,
I ignored the warnning & tried to save top & crd file by saveamoebaparam
but it Sleap gets core damped.
I think ,it is problem with .lib file in defining sp2 carbon as
"CA"(with other force fields it is working fine ).Could
you please suggest me how to define sp2 carbon of nanotube in .lib file to
be identified by force field.
thanks

With regrads,
Hemant Kumar
Graduate Student
CCMT,Department of Physics
IISC,Bangalore

On Fri, 6 Mar 2009, Wei Zhang wrote:

> 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_at_physics.iisc.ernet.in>
>> Date: Fri, March 6, 2009 3:00 pm
>> To: amber_at_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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