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Bug #147

pdb2gmx fails to generate pr-files when no water is present

Added by Erik Marklund over 12 years ago. Updated over 12 years ago.

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

When I issue the command:

pdb2gmx -f _10naked.pdb -o i -p i -i i -vsite hydrogens -water spce

using the AMBER03-port, no i_[AB]_pr.itp files are generated. Now, if I do the
same thing with _10ns.pdb such files are generated. _10ns.pdb and _10naked.pdb
both contain the same DNA molecule, but _10ns.pdb also contains solvent and
ions. In fact, _10naked.pdb was made by executing "grep -v -e SOL -e Na -e Cl
_10ns.pdb > _10naked.pdb".

This problem arises under gmx 3.3.2b and 4.0. I'll provide the relevant files.

_10naked.pdb (33.2 KB) _10naked.pdb DNA only Erik Marklund, 04/23/2007 11:49 AM
_10ns.pdb (704 KB) _10ns.pdb DNA, water and ions Erik Marklund, 04/23/2007 11:50 AM

History

#1 Updated by Erik Marklund over 12 years ago

Created an attachment (id=183)
DNA only

Will not give rise to pr-files.

#2 Updated by Erik Marklund over 12 years ago

Created an attachment (id=184)
DNA, water and ions

Gives me pr-files

#3 Updated by Erik Marklund over 12 years ago

Note that the problem remains without the -vsite flag. Therefore I won't upload
my ddb-file.

#4 Updated by Erik Marklund over 12 years ago

It seems that the pr-block is present after all. In the case of the naked DNA
the pr-block was synonymous with the file i.itp, #included from i.top. When
solvent was present in the pdb-file i_[AB]_pr.itp contained the pr-block and was
#included from i.itp. I just got confused by this inconsistency, or whatever you
may want to call it.

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