Thanks everyone. So I would start with changing the compilation option Jean suggested and then think about changing more stuff in the code.
But how and where should I change those compilation options? Should I change them prior to configuring?
Thanks,
Hamed S. Hayatshahi
PhD student of Medicinal Chemistry
University of Utah
سيد حامد سادات حياتشاهي
دانشجوي دكتراي شيمي دارويي
دانشگاه يوتا
On Jul 22, 2013, at 1:38 AM, Jean-Paul Becker <jpb.q4md-forcefieldtools.org> wrote:
> Dear Hamed,
>
> 1. Regarding your first question, I would change the compilation
> option for resp and try something like:
> -mcmodel=medium or even -mcmodel=large
> That will change the way memory is handled and should
> allow for larger arrays of data.
>
> 2. Regarding your second question, you figured it out right:
> - maxmol is the maximum number of molecules.
> - maxq is the maximum number of charge centers of all molecules
> considered together.
> - maxlgr is the maximum number of charge constraints you want
> to apply.
> You have to consider in this number not only the charges imposed
> to each molecule of your set but also all the intra- and inter-molecular
> charge constraints.
>
> I hope this helps.
> Cheers.
> JPB.
>
>
>
> "Hamed S. Hayatshahi" <biophysicist1981.yahoo.com> a écrit :
>
>> Hi
>>
>> I am about to do a resp charge fit (using R.E.D. script) for totally
>> 276 molecules (46 conformations each with 6 reorientations) each
>> having 65 atoms which make totally 17940 centers. As expected, the
>> resp cannot handle these many centers with its default maxq value
>> defined in $AMBEHOME/AmberTools/src/etc/limits.h. So I increased the
>> values and recompiled amber (amber12 with ambertoolds13). But when I
>> go beyond "maxq=8000, maxlgr=2900 and maxmol=300", amber
>> installation fails at "make install" step finishing with the
>> following lines:
>>
>> 235/amber-em/amber12/include -shared-intel \
>> lapack.o resp.o -o resp
>> resp.o: In function `MAIN__':
>> resp.F:(.text+0x130): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0x13b): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.o: In function `readin_':
>> resp.F:(.text+0x58b): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0x5a9): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0x5b3): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0xb1f): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0xb51): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0x10a2): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0x1108): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0x112d): relocation truncated to fit: R_X86_64_PC32
>> against symbol `infoa_' defined in COMMON section in resp.o
>> resp.F:(.text+0x14b2): additional relocation overflows omitted from
>> the output
>> make[2]: *** [resp] Error 1
>> make[2]: Leaving directory
>> `/uufs/chpc.utah.edu/common/home/u0723235/amber-em/amber12/AmberTools/src/etc'
>> make[1]: *** [serial] Error 2
>> make[1]: Leaving directory
>> `/uufs/chpc.utah.edu/common/home/u0723235/amber-em/amber12/AmberTools/src'
>> make: *** [install] Error 2
>>
>>
>> Then all tests fail in "make test" step. I used ./configure intel.
>> Now, two questions:
>>
>> 1- Is there anyway that I can go beyond the mentioned limits,
>> especially maxq > 8000?
>>
>> 2- I think maxq is the max number of centers and maxmol is the max
>> number of molecules; but I am not sure what maxlgr is and how it
>> should be balanced with other values? There is an advice in a
>> discussion in 2009
>> (http://structbio.vanderbilt.edu/archives/amber-archive/2009/3026.php) to
>> pay attention to the multiple occurrences of these values in resp.F,
>> but I couldn't understand why and how is it important?
>>
>> Thanks for the help;
>> Hamed S. Hayatshahi
>> Graduate Student of Medicinal Chemistry
>> University of Utah
>> +1 (801) 807 4121
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
> --
> Jean-Paul Becker
> Equipe THERA
> Laboratoire des Glucides
> FRE 3517
> 1 rue des Louvels
> 80036 Amiens Cedex
> France
>
>
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Received on Mon Jul 22 2013 - 11:00:02 PDT
