Project

General

Profile

Bug #2151

gmx solvate fails with solvent pdb (not gro) file

Added by Berk Hess almost 3 years ago. Updated almost 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
Affected version:
Difficulty:
simple
Close

Description

gmx solvate -cp conf.gro -scale 0.35 -cs ow.pdb -o solv.pdb
results in a segv. pdinfo is accessed one beyond its size. The pdbinfo check in addAtom (called from removeMarkedAtoms) seems to be incorrect. It seems that the solvent atoms data, of 216 atoms, gets indexed with the index of the fully solvated system. This can never have worked. Converting the solvent pdb to gro circumvents this issue, since then there is no pdbinfo.

Failed to read a valid object file image from memory.
0x0000000000867f3f in gmx::AtomsBuilder::addAtom (this=0xffefff020, atoms=...,
i=216) at /home/hess/gmx_master/src/gromacs/topology/atomsbuilder.cpp:125
atoms_->pdbinfo[index] = atoms.pdbinfo[i];

(gdb) p atoms
$1 = (const t_atoms &) @0x6bcbb30: {nr = 216, atom = 0x6bfec20,
atomname = 0x6c32080, atomtype = 0x0, atomtypeB = 0x0, nres = 217,
resinfo = 0x6c3d700, pdbinfo = 0x6bd7560, haveMass = 0, haveCharge = 0,
haveType = 0, haveBState = 0, havePdbInfo = 1}

conf.gro (454 Bytes) conf.gro Berk Hess, 04/07/2017 02:55 PM
ow.pdb (16.9 KB) ow.pdb Berk Hess, 04/07/2017 02:56 PM

Related issues

Related to GROMACS - Bug #2148: gmx solvate crashing or leaving gaps for hexagonal solvent boxClosed

History

#1 Updated by Teemu Murtola almost 3 years ago

  • Related to Bug #2148: gmx solvate crashing or leaving gaps for hexagonal solvent box added

#2 Updated by Teemu Murtola almost 3 years ago

  • Status changed from New to Feedback wanted
  • Assignee changed from Teemu Murtola to Berk Hess
  • Target version set to 2016.4

I think this has already been fixed in release-2016 (after being one of the things affecting #2148).

#3 Updated by Berk Hess almost 3 years ago

  • Status changed from Feedback wanted to Resolved

Ah, yes. I looked at #2148 before submitting, but didn't realize there was already a fix in release-2016 that fixed also this issue. And this has not been merged into master yet, so I still noticed it there.
Thanks.

#4 Updated by Mark Abraham almost 3 years ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF