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
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Received on Sun Jul 21 2013 - 19:00:02 PDT
