VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Apr 19 2016 - 19:38:54 CDT

Scratch that last response. I was looking at the wrong PDB file.

On Wed, Apr 20, 2016 at 12:33 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> So I haven't tested anything yet, but a skimming of the files you sent
> over shows that the PDB you start of with (not sure if that is included or
> not) is probably not correct.
>
> Usually when you have multiple chains you should have a "TER" flag
> separating one chain from the next. I am guessing you were either missing
> this or something else. The reason why I say this is that your PSF shows a
> BOND between your chain A and Chain B --- atom 1413 connected to 1415 --
> line 84040 of the PSF file. This should not happen since the chains are not
> covalantly linked -- if they were it would be one giant protein.
>
> Look into this "TER" separation of PDB so as to ensure that the chains are
> not bonded in the PSF. I am not sure if this will solve the solvation
> problem or not - but it might -- will test in detail shortly and see if I
> can find a fix.
>
> Best,
> /A
> ​
> 

-- 
Best,
/A