Dear AMBER users,
In my protein of interest, there are two chains A & B.
In chain A, there are several Cysteine residues disulfide bonded with in the
same chain. Also the same for chain B Cys residues.
In the PDB file, to make the disulfide bridges, I changed all the CYS to CYX
and then proceeded for tleap with the following commands:
> NF = loadpdb NF.pdb
Loading PDB file: ./NF.pdb
Added missing heavy atom: .R<CGLY 197>.A<OXT 8>
total atoms in file: 1511
Leap added 1438 missing atoms according to residue templates:
1 Heavy
1437 H / lone pairs
> bond NF.7.SG NF.31.SG
> bond NF.10.SG NF.60.SG
> bond NF.28.SG NF.82.SG
> bond NF.32.SG NF.84.SG
> bond NF.59.SG NF.87.SG
(for the first one where NF is UNIT, 7 is the residue number in chain A and
SG is the atom && NF is UNIT, 31 is the residue number in chain A and SG is
the atom)
These are all Cys atoms bonded in Chain A.
But when I tried with the Chain B residues, the tleap complains like
follows:
> bond NF.3.SG NF.51.SG
bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
>
(for the first one where NF is UNIT, 3 is the residue number in chain B and
SG is the atom && NF is UNIT, 51 is the residue number in chain B and SG is
the atom)
In the PDB file, I have re-checked the two atoms from the Cys-3 and Cys-51
from chain B. It all like that of chain A.
But tleap doesnt understand this. Why ??
Is there any tricky way to give the input in tleap/xleap for chain-A and
chain-B diferentially?
Thank you for your suggestions.
--
Siddharth Rastogi
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Received on Tue Feb 02 2010 - 17:30:03 PST
