VMD-L Mailing List

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Mon Oct 14 2019 - 07:51:30 CDT

Dear VMD users:

I have a protein that consist on two separated polipeptide chains connected
by a disulphide bond. I want to join them a a unique fragment to process it
with writetopgmx (topotools) to build the gromacs topology. I have tried
changing the segname and chain name of the protein so that both chains have
the same name and segname. However VMD still considers them as separated
chains. I checked on the psf that the inter-chain S-S bond is present and
it is. How can I get VMD to understand that these chains are connected so
they can be treated as one fragment?

Thanks.

--------------------------------------------
Raul R Araya-Secchi
Postdoctoral researcher
X-ray and Neutron Science,
The Structural Biophysics Group,
Universitetsparken 5,
2100 CPH, DK.
raul.secchi_at_nbi.ku.dk