Hi Jean
Thanks. I already did that on the original amber12 resp.F and the installations problem seems to be solved.
Now I wanna test to see if RED works on my big system. Previously, RED worked until it prepared all conformations which took a long time and then quitted with the error. I want RED script to use the already prepared conformation log files to avoid wasting time and allocation. Is there any version of RED script to do that for me, or I need to hack the script myself?
Thanks again.
Hamed S. Hayatshahi
PhD student of Medicinal Chemistry
University of Utah
سيد حامد سادات حياتشاهي
دانشجوي دكتراي شيمي دارويي
دانشگاه يوتا
On Jul 23, 2013, at 2:46 AM, Jean-Paul Becker <jpb.q4md-forcefieldtools.org> wrote:
> Hi Hamed,
>
> You are welcome.
> You may go the easy way and download the standalone version
> of RESP from our web site at:
> http://q4md-forcefieldtools.org/RED/resp/
> (You will find the download link at the bottom of the page)
> You will have to:
> - correct the maxq and maxmol parameters
> in each routine (likely 15 corrections for each of them)
> - edit the Makefile to choose your Fortran compiler
> and add the -mcmodel=medium option when required.
>
> We are currently developing a new version of RESP
> that will bring new functionalities devoted to the assessment
> of the fit quality.
> In this new version all the values of these parameters
> (maxq, maxmol...) will be determined in a single place
> to avoid the annoyance of going through the whole code
> to change them.
>
> Cheers.
> JPB.
>
> "Hamed S. Hayatshahi" <biophysicist1981.yahoo.com> a écrit :
>> 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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jean-Paul Becker
> Equipe THERA
> Laboratoire des Glucides
> FRE 3517
> 3 rue des Louvels
> 80036 Amiens Cedex
> France
>
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Received on Tue Jul 23 2013 - 09:30:02 PDT
