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Bug #465

pdb2gmx with DNA

Added by George Patargias about 10 years ago. Updated about 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

I am trying to generate a topology of a dna strcture using the charmm dna.rtp file
and the Gromacs git version.

With default selections for the -ter flag (i.e termini charged) I get the message:

Program pdb2gmx, VERSION 4.0.99-dev-2010-07-07 08:35:28 -0700-7cbc3b9-dirty
Source code file: pdb2top.c, line: 922

Fatal error:
atom N not found in buiding block 2DG while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

With selection NONE for the -ter flag, I get the message

Program pdb2gmx, VERSION 4.0.99-dev-2010-07-07 08:35:28 -0700-7cbc3b9-dirty
Source code file: pdb2top.c, line: 887

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I attach the pdb file with the dna structure whose topology I am trying to generate

I would much appreciate your help.

mydna.pdb (73.2 KB) mydna.pdb pdb file of a 16 base pair DNA George Patargias, 07/11/2010 01:00 AM

History

#1 Updated by George Patargias about 10 years ago

Created an attachment (id=489)
pdb file of a 16 base pair DNA

#2 Updated by David van der Spoel about 10 years ago

I reproduced this. How should the termini be treated? Does it work if you add the missing atoms? Or are all the atoms there already? In that case it is a bug. Gromacs does not add any H to DNA or RNA if they are missing.

#3 Updated by George Patargias about 10 years ago

I am not sure what atoms are missing.

As far as I am concerned, I built all missing atoms (basically h's) with charmm,
so the termini are already treated the way they should be (for DNA). I think that
the uploaded pdb has all the atoms.

All I want is to make a top file. I quess that something could be changed in the
pdb2gmx.c or/and pdb2top.c to get rid of the error but, obviously, dont know what.

Best wishes
George

(In reply to comment #2)

I reproduced this. How should the termini be treated? Does it work if you add
the missing atoms? Or are all the atoms there already? In that case it is a
bug. Gromacs does not add any H to DNA or RNA if they are missing.

#4 Updated by Erik Lindahl about 10 years ago

Fixed. We have added proper residue termini translation tables for Charmm27, and also improved pdb2gmx so it doesn't try to apply amino acid termini. Applied in git master.

#5 Updated by George Patargias about 10 years ago

Many thanks for this.

Best wishes
George

(In reply to comment #4)

Fixed. We have added proper residue termini translation tables for Charmm27,
and also improved pdb2gmx so it doesn't try to apply amino acid termini.
Applied in git master.

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