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Bug #171

Error in pdb2gmx version 3.3.1

Added by Justin Lemkul about 12 years ago. Updated about 12 years ago.

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

Description

In running pdb2gmx in GMX 3.3.1, I receive the following error.

The command issued was:

$ pdb2gmx -f AB40.pdb -o AB40.gro -ignh

(normal messages from pdb2gmx...)

-------------------------------------------------
Program pdb2gmx, VERSION 3.3.1
Source code file: pgutil.c, line: 87

Fatal error:
Atom N not found in residue 1 while adding improper


The PDB file I am trying to process is attached to this report. I have worked with it before using GMX 3.3 with no problem. The force field I am trying to use is ffG43a1, but the problem occurs with every force field except for ffgmx.

AB40.pdb (47.2 KB) AB40.pdb The PDB file I am trying to process. Justin Lemkul, 10/16/2007 10:35 PM

History

#1 Updated by Justin Lemkul about 12 years ago

Created an attachment (id=249)
The PDB file I am trying to process.

#2 Updated by David van der Spoel about 12 years ago

I can not reproduce the problem with either 3.3.1 or 3.3.2. What computer system are you using? How did you compile?

#3 Updated by Justin Lemkul about 12 years ago

The computer is from Monarch Computer Systems, 64-bit Opteron processor, running
Linux Ubuntu 7.04 (Linux kernel 2.6.20); gcc is version 3.3. I compiled
according to the normal procedure, as I recall (it's been a while).

./configure
make
make install

#4 Updated by David van der Spoel about 12 years ago

Then a compile error seems unlikely. However are you sure the program you use is the one you think it is? Check with
which pdb2gmx

There are Ubuntu packages for gromacs as well.

Otherwise, check the file share/gromacs/top/ffG43a1-n.tdb, and see how it compares to other similar files, e.g. ffgmx-n.tdb.

#5 Updated by David van der Spoel about 12 years ago

Hi Justin,

have you tried running
which pdb2gmx
just to make sure you're using the one you think you are using?

#6 Updated by Justin Lemkul about 12 years ago

(In reply to comment #5)

Hi Justin,

have you tried running
which pdb2gmx
just to make sure you're using the one you think you are using?

The version is correct - 3.3.1. I went back into the records for the machine and found that the Ubuntu package was used to install Gromacs; it was not done from source. Perhaps something is wrong in that package? In any case, I am going to try to re-install from source and see if that fixes the problem.

#7 Updated by Justin Lemkul about 12 years ago

(In reply to comment #6)

(In reply to comment #5)

Hi Justin,

have you tried running
which pdb2gmx
just to make sure you're using the one you think you are using?

The version is correct - 3.3.1. I went back into the records for the machine
and found that the Ubuntu package was used to install Gromacs; it was not done
from source. Perhaps something is wrong in that package? In any case, I am
going to try to re-install from source and see if that fixes the problem.

Just to follow up - I re-compiled GMX 3.3.1 from source and it appears to have alleviated the problem. pdb2gmx now processes the .pdb file in question without any problems. Perhaps something is broken within the Ubuntu package.

#8 Updated by Erik Lindahl about 12 years ago

Problem seems to have been in Ubuntu.

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