Hi,
once again a small problem. After making the bond when I write the PDB file
by-
savapdb lig lig_tleapout.pdb
The lig_tleapout.pdb file has both the residues separated by TER. I am not
sure that tleap makes a bond in reality or not. Yes I can see the bond in
VMD when i load *.prm and *.crd file written by tleap but why doesnt tleap
writes molecule as one molecule as residue number 1 and 2.
thanks
mish
On Fri, Apr 1, 2011 at 8:07 PM, mish <smncbr.gmail.com> wrote:
> I tried it and figured out that tleap reads the exact reside number
> provided in the pdb file. It does not renumbers it from 1....and so on. Now
> its fine if I use > bond lig.268.C1 lig.267.O or rename the residue
> numbers to 1 and 2.
>
> Thanks
> ..mish
>
>
> On Fri, Apr 1, 2011 at 5:23 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> Use "desc lig" to get a description of the ligand (and "desc lig.1", "desc
>> lig.2", etc. to get residue-specific details).
>>
>> It looks like you may be getting the wrong residues (i.e. that residue 1
>> doesn't have C1, and residue 2 doesn't have O). You may also consider
>> putting a 1 at the end of the bond command as the bond order, but from the
>> usage statement that appears to be optional.
>>
>> Hope this helps,
>> Jason
>>
>> On Fri, Apr 1, 2011 at 6:20 AM, mish <smncbr.gmail.com> wrote:
>>
>> > Hi all:
>> > I have a small question about the making bond between two residues in
>> > tleap.
>> > I have fucose (0fA) and methyl (OME) residue in the PDB file and want to
>> > make a bond between C1 of 0fA and O of OME. I cant change the oder
>> residues
>> > in PDB because of some other reasons. I am trying to load the file and
>> > making a bond in between them by there is some error. Can any od you
>> > correct
>> > me please ? where as I am making a bond like source leaprc.GLYCAM_06
>> >
>> >
>> ----------------------------------------------------------------------------------------------------------------------------------
>> > source leaprc.ff99SB
>> > lig=loadpdb lig1.pdb
>> > bond lig.1.C1 lig.2.O
>> > savepdb RSL lig_out.pdb
>> > saveamberparm lig lig.prmtop lig.prmcrd
>> > quit
>> >
>> >
>> ----------------------------------------------------------------------------------------------------------------------------------
>> > Its hows the eroor :
>> > bond: Argument #1 is type String must be of type: [atom]
>> > usage: bond <atom1> <atom2> [order]
>> >
>> >
>> > PDB file looks like :
>> > ATOM 3928 C1 0fA 268 -2.092 12.828 14.170 1.00 0.00
>> > ATOM 3929 H1 0fA 268 -1.517 12.455 15.033 1.00 0.00
>> > ATOM 3930 O5 0fA 268 -1.319 12.709 13.013 1.00 0.00
>> > ATOM 3931 C5 0fA 268 -2.016 13.107 11.804 1.00 0.00
>> > ATOM 3932 H5 0fA 268 -2.393 14.142 11.903 1.00 0.00
>> > ATOM 3933 C6 0fA 268 -1.015 13.079 10.678 1.00 0.00
>> > ATOM 3934 H61 0fA 268 -1.542 13.294 9.746 1.00 0.00
>> > ATOM 3935 H62 0fA 268 -0.664 12.053 10.544 1.00 0.00
>> > ATOM 3936 H63 0fA 268 -0.193 13.757 10.923 1.00 0.00
>> > ATOM 3937 C4 0fA 268 -3.191 12.186 11.596 1.00 0.00
>> > ATOM 3938 H4 0fA 268 -3.728 12.494 10.688 1.00 0.00
>> > ATOM 3939 O4 0fA 268 -2.681 10.873 11.431 1.00 0.00
>> > ATOM 3940 H4O 0fA 268 -2.193 10.624 12.216 1.00 0.00
>> > ATOM 3941 C3 0fA 268 -4.119 12.270 12.824 1.00 0.00
>> > ATOM 3942 H3 0fA 268 -4.378 13.333 12.934 1.00 0.00
>> > ATOM 3943 O3 0fA 268 -5.299 11.488 12.700 1.00 0.00
>> > ATOM 3944 H3O 0fA 268 -5.909 11.731 13.423 1.00 0.00
>> > ATOM 3945 C2 0fA 268 -3.327 11.927 14.059 1.00 0.00
>> > ATOM 3946 H2 0fA 268 -2.908 10.907 13.992 1.00 0.00
>> > ATOM 3947 O2 0fA 268 -4.202 12.050 15.232 1.00 0.00
>> > ATOM 3948 H2O 0fA 268 -4.712 12.857 15.177 1.00 0.00
>> > TER
>> > ATOM 3923 H1 OME 267 -2.008 15.976 14.892 1.00 0.00
>> > ATOM 3924 CH3 OME 267 -1.549 15.020 14.665 1.00 0.00
>> > ATOM 3925 H2 OME 267 -0.960 14.655 15.500 1.00 0.00
>> > ATOM 3926 H3 OME 267 -0.888 15.092 13.808 1.00 0.00
>> > ATOM 3927 O OME 267 -2.562 14.144 14.396 1.00 0.00
>> > END
>> >
>> >
>> > Thanking You
>> > ..mish
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Apr 20 2011 - 10:00:03 PDT
