Hamed,
A last point: when modifying parameters in the RESP program, we always
keep a resp version without modification:
We compare the results obtained (without vs with modifications) in a
multiple molecule charge fit (fit that can be done by the two RESP
binaries).
For the molecular system, which requests the modifications we also
compare the charge values obtained in each single molecule fit vs the
multiple molecule fit.
Without inter-molecular charge constraint and without inter molecular
charge equivalencing the differences should be of +/- 1.10-4 or so...
It cost nothing and can avoid many side effects ;-)
regards, Francois
> Actually I used the Amber12 resp.F with modified limits in limits.h
> with -mcmodel=large, before Jean suggested me to use your resp
> version, and it worked. So is there any specific reason that you
> suggest me to use it instead of the original version?
> It seems that the values used in Amber12 resp.F are commented out;
> although I don't know fortran! However, it worked.
> No I am not sure about the amount of RAM it can get in my machine
> and I don't have chance to check it with "top" as it is killed
> immediately.
> Maxq=20000 is enough for my case, but I am curious about the upper
> limits because I am thinking about having bigger systems in near
> future...
> On Jul 24, 2013, at 12:06 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Hamed,
>>
>>> Just to verify,
>>> Recompiling resp with -mcmodel=large as Jean advised, worked for me,
>>> but it seems that changing the values in limits.h is enough and
>>> there is no need to change all the maxq, maxlgr and maxmol values in
>>> resp.F.
>>
>> My understanding is that you can_not_ modify the values of maxq,
>> maxlgr and maxmol in 'resp.F' (from the AmberTools & you have to apply
>> these corrections in 'src/etc/limits.h'); while you have to do it in
>> 'resp.f' in the standalone version of the RESP program we provide.
>>
>>> However, when I raised them to extreme
>>> (maxq=50000,maxlgr=10000,maxmol=1000) values in limits.h, the
>>> installation succeeded, but running resp immediately terminated with
>>> "Killed" prompt which seems to be a real memory isuue and I think
>>> it is machine-dependent.
>>
>> are you sure you have the requested amount of RAM in the machine you use?
>>
>>> So when I relaxed the parameters to maxq=20000, maxlgr=2900 and
>>> maxmol=300 (which is good enough for my problem), everything seemed
>>> to be fine.
>>
>> well if maxq=20000, maxlgr=2900 and maxmol=300 work for you why
>> increasing these values even more?
>>
>> regards, Francois
>>
>>
>>> 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
>>>>> ??? ???? ????? ????????
>>>>> ??????? ?????? ???? ??????
>>>>> ??????? ????
>>>>>
>>>>> 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?
>>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 25 2013 - 00:30:02 PDT
