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

Yang Ye leafyoung81-group at yahoo.com
Thu Feb 2 11:38:34 CET 2006

To eliminate O2*, check xlateat.dat under top of share directory of Gromacs.
It is a replacement table. To fix arbitrary PDB file, checking the rtp file
from FF usually helps.


Yang Ye


From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Tsjerk Wassenaar
Sent: Thursday, February 02, 2006 2:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] converting pdb to gmx successfully - how?


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,


On 2/1/06, David Mathog <mathog at caltech.edu> wrote:

Short version:

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.


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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