[gmx-users] converting pdb to gmx successfully - how?

[Ken Rotondi]

TER statements are insufficient, you need chain identifiers.

Ken

On Feb 2, 2006, at 1:59 AM, Tsjerk Wassenaar wrote:

> Hi David,
>
> Yeah, wouldn't we all want to be able to take arbitrary pdb files, run 
> them through a black box, fixing missing atoms, residues, deviations 
> from naming conventions, etc, etc. But, to cope with reality rather 
> than ideality, you can try to run the structure after (4) through 
> pdb2gmx using the option -ignh. If you then still have long bond 
> warnings, this either means that your structure misses stretches of 
> residues or that seperate chains are being connected. The latter you 
> can deal with by assigning chain identifiers, though introducing TER 
> statements should also work. You can find more practical notes on 
> using Gromacs with DNA/RNA in the Gromacs user list archive.
>
> Good luck,
>
> Tsjerk
>
> On 2/1/06, David Mathog <mathog at caltech.edu> wrote:
>>
>> I want to be able to feed an arbitrary pdb file through
>> some program such that pdb2gmx will accept the result.
>> What is "some program"???
>>
>> Long version:
>>
>> I'm having trouble getting a structure with DNA and protein
>> through pdb2gmx.  Initially this began with warnings about "atom O2* 
>> is
>> missing".  Attempts to fix that broke the protein part.  The PDB spec
>> says that columns 18-20 are the residue name.  The topology file
>> says to use ADE for the RNA form and DADE for the DNA (etc.)  DADE
>> won't fit in 3 characters so presumably pdb2gmx accepts some other
>> broader syntax for a "PDB" file.
>>
>> 0.  pdb2gmx doesn't know what C,G,T,A sre.
>>
>> 1.  Try the RNA forms (A->ADE etc) in cols 18-20, see if it
>> autodetects DNA.  Nope, O2* messages.
>>
>> 2.  Add a D in col 17.  Result same as 1.
>>
>> 3. Leave a space in column 17 and put DADE in 18-21.  This
>> A: breaks the PDB file format
>> B: eliminated the O2* warnings
>> C: left the H4 and H6 warnings (Xray structure, so of course
>>   no hydrogens)
>> D: emitted a ton of "Warning: Long Bond" message for many, many
>> pairs of atoms in the nucleic acid part of the file.
>>
>> 4.  Ran the pdb file through pdb2pqr web server.  Then
>> changed A->ADE,etc, ran that through pdb2gmx, and this time
>> no warnings or errors (in the nucleic acid part).
>>
>> 5.  Took the pdb file from 4 and changed ADE->DADE (breaking PDB
>> format).  This worked the same as 4.
>>
>> Then I realized pdb2gmx was just blowing up in 4,5 because
>> pdb2pqr was introducing an HA on the first LYS, so it wasn't
>> even getting to the nucleic acid parts, which pdb2pqr moved to
>> the end of the file (they were at the front before.)
>>
>> 6. Found "protonate".  Tried running the PDB file from (3) through
>> it with:
>>
>>  protonate -s dpeptide1
>>
>> which blew up when 0 (system) was selected with:
>> Fatal error:
>>
>> Atom -C not found in residue LYS39 while adding hydrogens
>>
>> --------------------------------------------------------
>>
>> At which point I gave up and wrote this note.
>>
>> Thanks,
>>
>> David Mathog
>> mathog at caltech.edu
>> Manager, Sequence Analysis Facility, Biology Division, Caltech
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>
>
>
> -- 
>
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
>  Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
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