AMBER Archive (2009)

Subject: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"

From: Sushil Mishra (sushilbioinfo_at_gmail.com)
Date: Wed Jul 15 2009 - 05:36:26 CDT

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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