Hi,
I think there's a bug in the function transformSecondaryStruct (I have
AmberTools 1.4 with bug fixes up to #16 here). In PTRAJ_PRINT mode
structInfo->filename is concatenated with a file suffix but as far as I
can tell from the code structInfo->filename may not be big enough and
strcat will happily overwrite subsequent memory.
/*
* ACTION: PTRAJ_PRINT
*/
structInfo = (transformSecondaryStructInfo *) action->carg1;
if (structInfo->filename != NULL)
outFile = safe_fopen(strcat(structInfo->filename, ".sum"), "w");
else
outFile = stdout;
There is still a problem in transformWatershell (I have reported that a
while back). The function assumes that :WAT should be used as
the default water residue. This will fail with a segmentation fault if
no such residue exists (I tried this with a PSF file).
buffer = getArgumentString(argumentStackPointer, NULL);
if (buffer != NULL)
info->solventMask = processAtomMask(buffer, action->state);
else
info->solventMask = processAtomMask(":WAT", action->state);
safe_free(buffer);
Cheers,
Hannes.
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Received on Mon Mar 14 2011 - 09:00:02 PDT
