Re: [ModPipe-users] MODELLER bug report

[Marco Galardini <>]

Hi Ben,

thanks for your prompt reply: the problem is that the PSSM file should 
be ok.

the conf file has these values:

XPRF_LIST       /nfs/[...]/modpipe-2.2.0/dbs/pdb95/db/pdb95_prf.list
XPRF_PSSMDB     /nfs/[...]/modpipe-2.2.0/dbs/pdb95/db/pdb95_prf.pssm

the files in that location are there and not empty:

$ ls -lh
total 1.3G
-rw-r--r-- 1 [...] [...] 3.7M Jun  5 09:53 pdb95_prf.list
-rw-r--r-- 1 [...] [...] 1.1G Jun  5 09:55 pdb95_prf.pssm

$ head -n 1 pdb95_prf.list
/nfs/[...]/modpipe-2.2.0/dbs/pdb95/data/2a/12asA/12asA-uniprot90.prf

$ head  pdb95_prf.pssm
/nfs/[...]/modpipe-2.2.0/dbs/pdb95/data/2a/12asA/12asA-uniprot90.prf
     327
   583   405   409   421   336   436   371   355   421   355   386 
450   386   421   386   646   471   379   286   336
   336   336   286   318   690   286   492   409   318   409   409 
318   268   353   318   336   336   386   518   764
   357   347   256   280   392   216   261   700   412   520   507 
267   266   289   292   311   357   567   260   349
   468   258   588   583   268   280   622   310   348   496   335 
356   287   588   396   509   394   339   224   306
   363   298   346   416   286   286   340   334   550   458   383 
381   329   668   495   430   646   354   281   314
   374   274   434   566   282   321   420   294   470   365   421 
420   371   760   466   421   374   332   319   369
   377   221   403   602   226   303   322   379   573   343   327 
337   288   721   516   342   452   408   223   274
   663   318   353   580   255   372   455   285   458   294   322 
331   320   602   443   400   404   334   235   291

Any other parameter or file I should look for?

Many thanks,
Marco

On 05/06/2014 19:55, Ben Webb wrote:
> On 6/5/14, 6:03 AM, Marco Galardini wrote:
> > *alloc_p_215E> Dynamic memory allocation failed.**
> > **              Routine, variable, status:  ipssm         3**
>
> This happens if you give Modeller an empty PSSM database (it tries to 
> allocate 0 bytes of memory to store it). It's already "fixed" in the 
> upcoming 9.14 release, in that it'll give you a more intelligible 
> error message, but the underlying cause is that something is wrong 
> with your PSSM file.
>
>     Ben