Dear Navanath Kumbhar,
If you want to generate new nucleotide fragments, you might look at
R.E.D. or R.E.D. Server. See
http://q4md-forcefieldtools.org/
& tutorials are also available.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
regards, Francois
> I want to do simulation of modified nuclesodies with anticodonloop
> structures by using sybyl mol2 file as input file format. I opened this file
> in xleap by using gaff force field but when i go to save it it gives
> for atom: .R<UNK0001 1 >. A < H108 285 > could not find type : H
>
> SO which force field i can use for to get top and crd files or any other
> procedure for that.
>
> Thanks and great regards
> from
> Navanath Kumbhar
> On Fri, Jun 11, 2010 at 6:39 AM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Thu, Jun 10, 2010, Navanath Kumbhar wrote:
>> >
>> > I want to creates .prepin and frcmod files for modified nucleosides by
>> using
>> > antechamber, for that i have taken sybylmol2 file as input for
>> antechamber,
>> > but it gives error as follows:
>> >
>> > $ antechamber -i wym.mol2 -fi mol2 -o wym.prepin -fo prepi -c bcc -s 2
>> >
>> > The atom number exceeds the MAXATOM,
>>
>> How many atoms are in your modified nucleoside? Remember that antechamber
>> is designed for single residues, or for drug-sized molecules.
>>
>> > Total number of electrons: 1383; net charge: 0
>> > INFO: Number of electrons is odd: 1383
>>
>> Antechamber only works for closed shell molecules. Do you have a net
>> charge
>> on your input molecule? If so, you must use the "-nc" option.
>>
>> Please work on smaller systems first, if at all possible. 1400 electrons is
>> a *lot*. Also, making parameters for *residues* (that will be linked to
>> others as a part of a polymer) is more complex than for an isolated
>> molecule.
>>
>> Also, be sure to check if what you need has already been done: the Amber
>> web
>> site has links to "modified nucleosides" and to "REDDB".
>>
>> ....dac
>>
>>
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>>
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>
>
F.-Y. Dupradeau
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Received on Fri Jun 11 2010 - 06:30:11 PDT
