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Bug #465

pdb2gmx with DNA

Added by George Patargias over 9 years ago. Updated over 9 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 over 9 years ago

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

#2 Updated by David van der Spoel over 9 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 over 9 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 over 9 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 over 9 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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