Re: [PyMOL] how to connect to atoms?

[Tsjerk W. <ts...@gm...>]

Hi Leila,

Are the peptides already positioned correctly? Then there's nothing you can
do with Pymol to help out with Gromacs. With Gromacs, you'll have to make a
special bond to account for the link between the peptides, and you have to
merge the two peptides during the processing with pdb2gmx. Check out
pdb2gmx and merging chains, and check out the specbond.dat file. There are
quite a few posts in the archive covering these issues. Probably searching
for isopeptide bond and/or ubiquitin lysine 63 will yield something.

Cheers,

Tsjerk

On Mon, May 11, 2015 at 9:25 PM, leila karami <kar...@gm...>
wrote:

> Dear pymol users
>
> I have one pdb file containing two peptides. Based on experimental data,
> I should connect two peptides to obtain one new peptide in pdb file. This
> connection is as follows:
>
> CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from
> peptide 2.
>
> How to make this connection using pymol without any change in the format
> of pdb file (after saving this file)? I want to use this new pdb file as an
> input file in gromacs package.
>
> Any help will highly appreciated.
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.