Dear Hamed,
> 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.
In this case look at the end of the RESP output file(s):
- output1_m1 (& output2_m1 if it exists) if you have a single P2N input file
and/or
- output1_mm (& output2_mm if it exists) if you have more than one P2N
input file
at the end of file(s) you should find a message related to maxq,
maxmol and/or maxlgr...
> 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?
I think I already answered to you in the q4md-fft mailing list about
this point:
- either you re-run the job in using the mode 2 (i.e. you skip the
geometry optimization step)
- or you try to use the 'Re_Fit' mode; in this case you need to have a
previous/successful R.E.D. job which has to be located in the $DIR
directory (# Directory name where the final data will be stored.)
if not you will have to rename all the files generated as they
should be in a successful job and create the corresponding file system
tree.
regards, Francois
> <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?
>>>>>
>>>>> 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
Received on Tue Jul 23 2013 - 23:00:02 PDT
