Dear Priya,
I saw your dimer's PDB file. But i guess you don't have a dimer.. the PDB
file you have given has same coordinates for both peptide chains...
And the bond thing that you saw using edit in LEaP is I GUESS you are
talking about another mistake in the pdb file where a space has come in
front of the coordinate values in line number 199-201 (residue 18) so PDB
file is read as
ATOM 193 CA ALA 18 2.039 2.062 1.486 1.00 0.00
ATOM 194 CB ALA 18 2.016 1.914 1.453 1.00 0.00
ATOM 195 C ALA 18 2.168 2.084 1.565 1.00 0.00
instead of
ATOM 193 CA ALA 18 20.392 20.621 14.865 1.00 0.00
ATOM 194 CB ALA 18 20.160 19.144 14.539 1.00 0.00
ATOM 195 C ALA 18 21.681 20.840 15.659 1.00 0.00
So i hope you need to have different coordinates to get the chains
differently... there would't be any problem from the TER card..
Cheers
On 3/15/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
>
> Dear All
> I am trying to run a simulation of dimer each chain has 16 residues.In the
> pdb fileI added TER between the chains but when i use the command edit in
> xleap there is a bond between the chains. but i want two different chains
> and non bonded. I am attaching the pdb file with mail.
> will anybody tell me the mistake.
> Thanks in advance
> Priya
>
>
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--
sandy_thesmitten
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Received on Sun Mar 18 2007 - 06:07:29 PDT
