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Bug #824

pdb2gmx does not generate cmap entries for alanine dipeptide

Added by Cesar Luis Avila over 5 years ago. Updated almost 3 years ago.

Status:
Closed
Priority:
Low
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

While processing a pdb containing the alanine dipeptide (ALAD), pdb2gmx does not generate the cmap entry in the topology file, although it is listed on the RTP.

aladipep.pdb - Alanine dipeptide (charmm ff) (1.54 KB) Cesar Luis Avila, 04/12/2012 10:41 AM

aladipep.pdb (1.75 KB) Cesar Luis Avila, 04/12/2012 02:36 PM

Associated revisions

Revision 41c86c01 (diff)
Added by Erik Lindahl almost 3 years ago

Fixed CMAP generation for alanine dipeptide special residue

Fix CMAP to work for residues not detected as proteins, and
make sure we correctly process single-residue entries that
have residue-internal CMAP definitions. In particular, this
is important for the default alanine dipeptide special
residues (ALAD) in Charmm27.

Fixes #824.

Change-Id: I5538b26175f12dcac983491323b5b6ee303c8434

History

#1 Updated by Roland Schulz over 5 years ago

  • Status changed from New to Feedback wanted

As you wrote on the mailing-list, all CMAP entries refer to the previous and the next residue. Thus no matching entry exists for a di-peptide. Should a di-peptide have a CMAP entry?

#2 Updated by Justin Lemkul over 5 years ago

Roland Schulz wrote:

As you wrote on the mailing-list, all CMAP entries refer to the previous and the next residue. Thus no matching entry exists for a di-peptide. Should a di-peptide have a CMAP entry?

In aminoacids.rtp of the latest charmm27.ff (in release-4-6), there is an alanine dipeptide (ALAD) entry, which has a [cmap] directive. Is the directive somehow not working, or is your input specifying something else?

#3 Updated by Cesar Luis Avila over 5 years ago

Justin:
pdb2gmx is using the default value -cmap yes, so I think the directive is not working.

Roland
CMAP was parametrized with alanine dipeptide (MacKerell 2004), so you must provide a cmap entry to reproduce the results.

#4 Updated by Rossen Apostolov over 5 years ago

Added Par to the watchers list since he implemented CMAP

#5 Updated by Pär Bjelkmar over 5 years ago

Nice, you seem to be on top of this. Cesar, could you please send me/post your input file and specify which gromacs version you're running?

Rossen Apostolov wrote:

Added Par to the watchers list since he implemented CMAP

#6 Updated by Rossen Apostolov about 5 years ago

Cesar, do you still have that problem?

#7 Updated by Cesar Luis Avila about 5 years ago

I haven't tried it with latest gromacs versions. I am attaching the pdb file so that it can be tested.

#8 Updated by Rossen Apostolov about 5 years ago

dialanine is actually a special case and you'll need to use ALAD as the residue name. have a look at charmm27.ff/aminoacids.rtp because the atom names are also a little different.

#9 Updated by Cesar Luis Avila about 5 years ago

Sorry, my mistake. I took the file from the wrong folder. This is the one that I was using as input for gromacs.

#10 Updated by Rossen Apostolov about 5 years ago

src/kernel/pdb2top.c says:

/* End loop at nres-1, since the very last residue does not have a +N atom, and * therefore we get a valgrind invalid 4 byte read error with atom am */
for(residx=0; residx<nres-1; residx++)
...

In your case there is only 1 residue, and that's why it fails. I'm not sure what's the proper way to work with that case.

#11 Updated by Teemu Murtola over 4 years ago

  • Status changed from Feedback wanted to New

Changed the status back to new as it seems that there is a problem. But it is still a bit unclear how well the underlying problem has been identified.

#12 Updated by Erik Lindahl about 3 years ago

  • Affected version set to 4.6

Neither of the two files uploaded by Cesar represent an alanine dipeptide - there is just a single CA atom.

#13 Updated by Erik Lindahl about 3 years ago

Never mind, it helps to read the text first. The second file is fine.

#14 Updated by Gerrit Code Review Bot about 3 years ago

Gerrit received a related patchset '1' for Issue #824.
Uploader: Erik Lindahl ()
Change-Id: I5538b26175f12dcac983491323b5b6ee303c8434
Gerrit URL: https://gerrit.gromacs.org/3665

#15 Updated by Erik Lindahl about 3 years ago

  • Status changed from New to Resolved

#16 Updated by Erik Lindahl about 3 years ago

  • Status changed from Resolved to Fix uploaded

#17 Updated by Gerrit Code Review Bot about 3 years ago

Gerrit received a related patchset '1' for Issue #824.
Uploader: Rossen Apostolov ()
Change-Id: Ifd92947c41a2498ec57e09dce8a8f1c0db2aeff4
Gerrit URL: https://gerrit.gromacs.org/3677

#18 Updated by Teemu Murtola almost 3 years ago

  • Category set to preprocessing (pdb2gmx,grompp)
  • Assignee set to Erik Lindahl
  • Target version set to 5.0

#19 Updated by Roland Schulz almost 3 years ago

  • Status changed from Fix uploaded to Closed

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