Hi,
It's possible that you got the residue numbers wrong or tleap have
renumbered the residues. I recommend cleaning the pdb file first with
*pdb4amber* before feeding it to leap. You can consult the documentation
for details.
Hope this helps.
Rashid
On Mon, Mar 5, 2018 at 5:46 PM, Jeyaram R A <ra.jeyaram.vit.ac.in> wrote:
> Dear Amber Users,
>
> In my interest of protein contains 7 disulfide bridges. I
> changed all the CYS residues name into CYX. On the tleap, to represent the
> disulfide bridge, I use the following command
>
>
> bond bnm.27.SG bnm.126.SG
>
> bond bnm.29.SG bnm.45.SG
>
> bond bnm.44.SG bnm.105.SG
>
> bond bnm.50.SG bnm.133.SG
>
> bond bnm.51.SG bnm.98.SG
>
> bond bnm.61.SG bnm.91.SG ?
>
> bond bnm.84.SG bnm.96.SG
>
>
> But, it shows as following
>
>
> bnm = loadpdb comp.pdb
>
> Loading PDB file: ./comp.pdb
> total atoms in file: 963
> Leap added 907 missing atoms according to residue templates:
> 907 H / lone pairs
> > bond bnm.27.SG bnm.126.SG
> bond: Argument #1 is type String must be of type: [atom]
> usage: bond <atom1> <atom2> [order]
> > bond bnm.29.SG bnm.45.SG
> bond: Argument #1 is type String must be of type: [atom]
> usage: bond <atom1> <atom2> [order]
>
> I don't know, why it happens, Help me to solve this problem.
>
> Thanks
> in advance
>
>
>
>
>
>
> .
>
> .
>
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Received on Mon Mar 05 2018 - 02:00:02 PST
