VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Wed Apr 20 2016 - 10:57:07 CDT

Thank you very much for helping me figure out the problem! I fixed the
original pdb file and I don't have this problem any longer. I checked
everything I could think of, but it didn't occur to me that this
column was shifted in the original file and created a protruding
error.

Thanks again!!

Olga

On Wed, Apr 20, 2016 at 1:29 AM, Ashar Malik <asharjm_at_gmail.com> wrote:
> 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