From: genie lfs (lfs.use_at_gmail.com)
Date: Mon Jun 14 2010 - 15:45:07 CDT

Hello,

I dont know how to perform this in VMD but i have done something like
this recently.

Choose any favorite programming language to replace all the CA atom
lines of villin.pdb from CA.pdb. The IUPAC name(the characters between
12 and 16) would help you here. Should not take much time if you are
familiar with the programming language.

But would be helpful to know if there is a way to perform this in VMD.

Thanks
Santhosh

On Mon, Jun 14, 2010 at 2:26 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> Dear all,
> I want to change only the carbon alpha coordinates of my vilin pdb
> file. The reason of doing that is to use the CA coordinates from a
> different pdb file as Targeted Molecular Dynamic target coordinates.
> I have two pdb files vilin.pdb which has all the initial coordinates
> and CA.pdb which only has the target CA coordinates. The residue index
> for the CA atoms is the same in both pdb file. However, atom indexes
> are different.
> Can anyone help me to change the CA coordinates in vilin.pdb to the
> ones in CA.pdb?
> Best,
> Mert
>
> mol load pdb vilin.pdb
> mol load pdb CA.pdb
>
> set s1 [atomselect 0 "name CA"]
> set s2 [atomselect 1 "name CA"]
> set s3 [atomselect 0 "protein"]
>
> I cant figure out the next step.
>