From: kong.winter (
Date: Thu May 03 2007 - 16:06:20 CDT

Hi all,

I'm eager to know how to conect two proteins with VMD.

A new paper (Eileen Puklin-Faucher et al., JCB 2006) said that:
The crystal structures of the v3 integrin in complex with an RGD-containing mimetic ligand (Protein Data Bank [PDB] code 1L5G) and of FNIII10 from the FNIII7-10 tetramer (PDB code 1FNF) were adopted to build the FNIII10Cv3 starting structure with the program VMD (Humphrey et al., 1996).

Step 1: the RGD tripeptides of the two separate structures were aligned
Step 2: then the mimetic ligand from the v3 structure was removed

How to do the two steps above in VMD ?
Any tips are appreciated,
thank you very much!