VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Apr 20 2016 - 00:29:41 CDT

OK, so what I see now is that assuming 0ps.pdb is the default pdb --

your PDB residue column is offset by 1 place.

Moving, for the first 9 residues, the residue numbers 1 column left - fixes
this issue. i.e.

|| ATOM 1 N THR A 1 29.972 78.277 67.795 1.00 0.00
|| ATOM 1 N THR A 1 29.972 78.277 67.795 1.00 0.00

the top line becomes the bottom line. Notice the residue number "1" moved 1
position to the left.

standard PDB record states that column

23 - 26 Integer Residue sequence number

in your case the first 9 residues are in column 27. VMD improvises and
prepends it with 0. (I am just guessing this -- I don't know why its
doing this)

But if you move the first 9 residues sequence numbers one position to
the left so they are contained inside column 23-26 --- everything will
work.

I am not sure what definitions of PDB format does the pdbplugin inside
VMD follows - but for now - moving one position works - maybe you can
wait for someone else to comment on this.

On Wed, Apr 20, 2016 at 12:38 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> 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
> 

-- 
Best,
/A