1. Make a file leapin_1 that says something like the following. This
creates ten molecules of b-D-Glcp-(1-4)-a-D-Glcp-OH. You might want
to change the translation coordinates. If someone knows a more
elegant way to specify the number of waters, please speak up.
=============================
leapin_1
=============================
set default write14scale on
source leaprc.GLYCAM_06
m01 = sequence { ROH 4GA 0GB }
m02 = sequence { ROH 4GA 0GB }
m03 = sequence { ROH 4GA 0GB }
m04 = sequence { ROH 4GA 0GB }
m05 = sequence { ROH 4GA 0GB }
m06 = sequence { ROH 4GA 0GB }
m07 = sequence { ROH 4GA 0GB }
m08 = sequence { ROH 4GA 0GB }
m09 = sequence { ROH 4GA 0GB }
m10 = sequence { ROH 4GA 0GB }
translate m02 { -10.0 0.0 0.0 }
translate m03 { 0.0 -10.0 0.0 }
translate m04 { 0.0 10.0 0.0 }
translate m05 { 10.0 0.0 0.0 }
translate m06 { 0.0 0.0 15.0 }
translate m07 { -10.0 0.0 15.0 }
translate m08 { 0.0 -10.0 15.0 }
translate m09 { 0.0 10.0 15.0 }
translate m10 { 10.0 0.0 15.0 }
ten_sacchs = combine { m01 m02 m03 m04 m05 m06 m07 m08 m09 m10 }
solvatebox ten_sacchs TIP3PBOX 1.0
savepdb ten_sacchs ten_sacchs_SOL.pdb
=============================
2. Run sleap (or tleap or xleap, etc.) on it using:
sleap -f leapin_1
3. Figure out which waters you want to keep. VMD might be helpful for this.
4. Copy ten_sacchs_SOL.pdb to ten_sacchs_200-SOL.pdb. Delete the
unwanted waters from ten_sacchs_200-SOL.pdb.
5. Make a file leapin_2 that looks something like the following. You
might want to alter the box dimensions, but havin it be a bit too big
should be ok (see step 6).
=============================
leapin_2
=============================
set default write14scale on
source leaprc.GLYCAM_06
whole_thing = loadpdb ten_sacchs_SOL_200.pdb
set whole_thing box { 40.0 40.0 40.0 90.0 }
saveamberparm whole_thing tenSol.top tenSol.rst
=============================
6. This one *MUST* be run with sleap if you are using Amber 11. If
it is a previous version of amber, be sure to set scee and scnb
properly in your input files.
sleap -f leapin_2
7. Minimize, at least for a few steps, at constant pressure to fix
the box size. (Anyone see an issue with this? I can't think of a
better way.)
8. Go ahead with whatever other simulation you had in mind.
:-) Lachele
On Thu, Sep 2, 2010 at 8:19 AM, subrata paul <paul.subrata34.gmail.com> wrote:
> dear Sir,
>
> I try to solve my problame by that procedure,but it does not work . Whan
> simulation is done the disaccharide molecule is dissociate.I do not found
> any clue .I am trying to read more tutorials for this but???please help me
> regarding this.
> thanking you
> subrata
>
> On Thu, Aug 26, 2010 at 9:18 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Subrata,
>>
>> > I am totaly new in amber. I am going through the tutorials. I am
>> able
>> > to creat .prmtop and .inpcrd file for a disaccharide using glycam force
>> > field in amber. Is it possible to creat .prmtop and .inpcrd for a
>> > disaccharide using amber force field.
>>
>> I do not understand why you want to use 'the' Amber FF for studying
>> carbohydrates as GLYCAM is devoted to this task. That being said, Yes,
>> you can and there are examples of such an approach in the literature.
>>
>> > I can simulate one disaccharide with solvatebox in amber. I want
>> to
>> > simulate 10 disaccharide and 200 water , but i don't know how i increase
>> > the number of disaccharide in the system and how i fixed the number of
>> water
>> > molecule?
>>
>> You could follow the approach below:
>>
>> xleap -f leaprc.GLYCAM_06
>> TT1 = sequence { XXX XXX YYY } # XXX being the sugar unit you need
>> savepdb TT1 TT1.pdb # YYY being the capping group
>>
>> The generated TT1.pdb PDB file with one disaccharide looks as it follows:
>> Cartesian coordinates of
>> XXX 1 residue 1
>> XXX 2 residue 2
>> YYY 3 residue 3
>> TER
>> END
>>
>> -------
>>
>> You copy TT1.pdb into TT2.pdb, you modify TT2.pdb as it follows
>> XXX 1 residue 1
>> XXX 2 residue 2
>> YYY 3 residue 3
>> TER
>> XXX 4 residue 4
>> XXX 5 residue 5
>> YYY 6 residue 6
>> END
>> Then you add +1 (or any value) to all X Cartesian coordinates of
>> residues 4, 5 & 6, keeping the Cartesian coordinates of residues 1, 2
>> & 3 unchanged.
>>
>> => You can load the double disaccharide TT2.pdb in leap:
>> xleap -f leaprc.GLYCAM_06
>> TT2 = loadpdb TT2.pdb
>> you can solvate, save prmtop/prmcrd files etc...
>>
>> -------
>>
>> same idea for three disaccharides:
>> XXX 1 residue 1
>> XXX 2 residue 2
>> YYY 3 residue 3
>> TER
>> XXX 4 residue 4 +1 to X Cart. coordinates
>> XXX 5 residue 5 +1 to X Cart. coordinates
>> YYY 6 residue 6 +1 to X Cart. coordinates
>> TER
>> XXX 7 residue 7 +2 to X Cart. coordinates
>> XXX 8 residue 8 +2 to X Cart. coordinates
>> YYY 9 residue 9 +2 to X Cart. coordinates
>> END
>>
>> etc...
>>
>> Then, instead of adding +1/+2 /+n to each X Cart. coordinates 2/3/n of
>> disaccharide you might choose more sophisticated translation values.
>>
>> regards, Francois
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 02 2010 - 10:00:02 PDT
