Hi,
Too happy to have been able to compile iAPBS and sander.APBS I have
tried to use it for an MMPBSA calculation via MMPBSA.py.
I had ran the simulations with pmemd.MPI from AMBER 11. The coordinate
files include only standard protein+DNA residues plus ACE and NME. The
force field was ff10.
Then, I got AMBER 12 and thus access to sander.APBS, which I wanted to
use to compare with the results previously obtained using PBSA. This is
my input for MMPBSA.py:
> Input file for running mmpbsa using APBS
> &general
> debug_printlevel=1,
> endframe=1000000000,
> entropy=0,
> interval=5,
> keep_files=1,
> ligand_mask=':1-69',
> netcdf=1,
> receptor_mask=':70-141,142-183',
> search_path=1,
> startframe=1,
> strip_mask=':WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+',
> use_sander=1,
> verbose=1,
> /
> &pb
> # for inp=1
> inp=1,
> # cavity_offset=0.86, not used by APBS
> cavity_surften=0.00542,
> radiopt=0,
> # for inp=2, which cannot be used with ff10 atom types...
> # inp=2,
> # cavity_offset=-0.5692,
> # cavity_surften=0.0378,
> # radiopt=1,
> exdi=80.0,
> fillratio=4.0,
> indi=1.0,
> istrng=0.15,
> linit=50000,
> prbrad=1.4,
> sander_apbs=1,
> scale=2.0,
> /
( If I set "sander_apbs=0", the same input works with PBSA, but only if
use sander from AMBER 11; with sander from AMBER 12 I get a problem with
atom radii)
The input generated for sander.ABPS is:
> File generated by MMPBSA.py
> &cntrl
> nsnb=99999, ioutfm=1, ntb=0,
> cut=999.0, imin=5, igb=6,
> /
> &apbs
> srfm=1, grid=0.5,0.5,0.5,
> ionc=0.15,0.15, pdie=1.0,
> ionq=1.0,-1.0, bcfl=2, nion=2,
> calc_type=0, sdie=80.0,
> gamma=0.02267728, ionrr=2.0,2.0,
> /
The first trajectory files are generated and sander.APBS starts running
on the complex. Then very quickly, MMPBSA.py fails with this error:
> Vpmg_ibForce: Forces *must* be calculated with spline-based surfaces!
> Vpmg_ibForce: Skipping ionic boundary force calculation!
> VASSERT: ASSERTION FAILURE! filename routines.c, line 1596, (Vpmg_ibForce(pmg, (*atomForce)[j].ibForce, j, pbeparm->srfm))
> forrtl: error (76): Abort trap signal
> Image PC Routine Line Source
> libSystem.B.dylib 00007FFF81AB70B7 Unknown Unknown Unknown
> CalcError: /a/progs/simu/amber12/bin/sander.APBS failed with prmtop ../../../../u1e2h2/u1e2h2_1_exdR_vac.prmtop!
>
>
> Exiting. All files have been retained.
I cannot see any obvious error in the output from sander.APBS that ends as:
> --------------------------------------------------------------------------------
> 4. RESULTS
> --------------------------------------------------------------------------------
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> TRAJENE: Frames in trajectory= 500
> TRAJENE: Atoms in trajectory= 3684
> minimizing coord set # 1
In principle srfm=1 means that I am requiring an 9-point harmonic
averaged surface, not a spline-based surface... Also, I tried to add
calcforce=1 (or even =2) to the input, but that does not solve the problem.
Any ideas?
Thanks!
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Le 07/12/12 10:39, Miguel Ortiz Lombardía a écrit :
> Hi Robert,
>
> You are absolutely right concerning compilers. Even if the intel
> compilers are "gcc compatible", they are so with gcc 4.2.1 and not with
> gcc 4.6.2, which I was using. To make sure I do not fall in runtime
> errors due to incompatibilities, I have recompiled the whole thing with
> the intel compilers (icc version 12.1.6 (gcc version 4.2.1 compatibility))
>
> The only changes required are at the configure steps:
>
> CC=icc CXX=icpc FC=ifort F77=ifort ./configure (...)
>
> I can confirm that this also succeeds compiling APBS / iAPBS / sander.APBS.
>
> Thanks!
>
> --
> Miguel Ortiz Lombardía
>
> Architecture et Fonction des Macromolécules Biologiques (UMR7257)
> CNRS, Aix-Marseille Université
> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
> Tel: +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
>
> Le 06/12/12 21:28, Robert Konecny a écrit :
>> Hi Miguel,
>>
>> that's a good news. I'm a bit surprised that your compilation succeeded
>> since it seems like you are using GNU compilers for APBS and iAPBS
>> compilation and then the Intel compilers for Amber. In my experience
>> compiler mixing rarely works.
>>
> (...)
>
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Received on Fri Dec 07 2012 - 05:30:02 PST
