If you download the "leap input file" you will see the instructions
the builder used to build the sucrose. Then, you can just add those
into a larger build. For example, in the one I just built (sucrose
can be built two ways), the file says:
amber_seq = sequence { 1GA 0CU }
The leap input file also loads a lot of other stuff, some of it not
relevant to sucrose, some of it required. Check out the message at
the link below for an example of how to generate a topology file
containing more than one molecule.
http://archive.ambermd.org/201009/0037.html
You should only need the first two steps unless you need to specify
the number of water molecules. You will need to add a "saveamberparm"
command to the first step.
If this is Amber 11, you must use sleap to generate your input files
and use the "set default write14scale on" directive in the input file.
If it is an earlier version of Amber, you should set scee and scnb
to 1.0 in your simulation control input files.
:-) Lachele
On Tue, Nov 23, 2010 at 8:27 PM, Jose Borreguero <borreguero.gmail.com> wrote:
> I used the Amber/Glycam input configurator
> tool<http://glycam.ccrc.uga.edu/AMBER>(
> http://glycam.ccrc.uga.edu/AMBER/) and obtained a topology file for the
> sucrose molecule. However, I have to simulate the sucrose in the presence of
> another molecule, so the topology file of the sucrose by itself will not do.
> Maybe there is a way of using the topology file in order to obtain the lib
> and frcmod files for the sucrose "residue", but I ignore it.
>
> - Jose
>
> On Tue, Nov 23, 2010 at 8:07 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
>
>> If you plan to use GLYCAM (and you probably should), there isn't a
>> specific frcmod or lib.
>>
>> See the section in the AmberTools manual on building oligosaccharides.
>> Is this Amber 11 or a previous version?
>>
>>
>> On Tue, Nov 23, 2010 at 5:56 PM, Jose Borreguero <borreguero.gmail.com>
>> wrote:
>> > Dear Amber users,
>> >
>> > Has anybody used the lib and frcmod files for sucrose ? I can't find them
>> > anywhere.
>> >
>> > Best regards
>> > Jose M. Borreguero
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Nov 23 2010 - 18:00:02 PST
