*Thanks alot Subhra,**I was generating the top and crd files but due to
wrong binding energy i thought this might be the problem.*
*Now i will again try simulation with the provided PDB. in case of
any trouble i will be in ur contact again.*
*thanking u.*
*sushil
*
On Wed, Jul 15, 2009 at 6:08 PM, Shubhra Gupta <shubhg.iiar.res.in> wrote:
> I have modified your given data. I have attached that as a pdb file.
> Try it directly in leap. It should generate topology and coordinates file.
>
> Shubhra
>
>
> On Wed, Jul 15, 2009 at 3:36 PM, Sushil Mishra <sushilbioinfo.gmail.com
> >wrote:
>
> > Hi all
> > First of all i would like u request you all that its my 4th request to
> all
> > but till not i havent reciened any responce..please suggest me coz its
> > urgent for me :-(
> > *I have a question about bond command. *i creation the structure of Alpha
> -
> > L - methyl-fucose by fallowing way so that leap can work.
> > HETATM 3926 C1 0fA d 0 5.820 15.924 -6.157
> > HETATM 3927 O5 0fA d 0 5.193 14.894 -6.908
> > HETATM 3928 C5 0fA d 0 3.763 14.922 -6.940
> > HETATM 3929 C6 0fA d 0 3.307 13.735 -7.786
> > HETATM 3930 C4 0fA d 0 3.188 14.880 -5.525
> > HETATM 3931 C3 0fA d 0 3.777 16.012 -4.700
> > HETATM 3932 C2 0fA d 0 5.291 15.936 -4.734
> > HETATM 3935 O2 0fA d 0 5.814 17.091 -4.054
> > HETATM 3936 H2O 0fA d 0 5.585 17.000 -3.136
> > HETATM 3937 O3 0fA d 0 3.325 15.858 -3.345
> > HETATM 3938 H3O 0fA d 0 3.703 15.049 -3.025
> > HETATM 3939 O4 0fA d 0 3.543 13.627 -4.920
> > HETATM 3940 H4O 0fA d 0 3.325 13.703 -4.000
> > TER
> > HETATM 3933 O OME d 0 5.491 17.154 -6.805
> > HETATM 3934 CH3 OME d 0 6.681 17.714 -7.315
> > END
> >
> > When i edit the structure, i see there is no bonding between ofA.C1 and
> > OME.O . i tried the simulation using same situation but results are not
> > correct. Binding energy for fucose is +ve which is not correct. Now i am
> > trying to create the single bond between ofA.C1 and OME.O by command
> > > bond 0fA.d.C1 OME.d.O "S"
> > it says
> > > bond: Argument #1 is type String must be of type: [atom]
> > usage: bond <atom1> <atom2> [order]
> >
> > please by watching the above pdb tel me exact command so that i can make
> a
> > bond between 0fA.C1 OME.O atoms. Had it been the problem in my previous
> > simulation ?? If it is nor possible to make a bond between atoms of
> > different units then what is the way to crate PDB for Alpha - L -
> > methyl-fucose. could any budy give me strusture.
> > Its too urgent for me ..please suggest me someting.
> >
> > sincerely
> > sushil k mishra
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--
Sushil K Mishra
Computational Chemistry Laboratory
National Centre for Biomolecular Research
ILBIT, Building A4 - 2.12
Kamenice 5
625 00 Brno
CZECH REPUBLIC
Tel. +420 549 492 521
Mob. +420 774 816 044
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Received on Wed Jul 15 2009 - 10:10:09 PDT
