[gmx-users] Re: mopac gcc g77 and x86_64
Gerrit Groenhof
ggroenh at gwdg.de
Tue Oct 30 15:49:16 CET 2007
dear Andrey,
include -lf2c (the fcc/gcc route) or -lg2c (fortran route) and see if
that resolves the problem.
Gerrit
> Message: 6
> Date: Tue, 30 Oct 2007 13:10:14 +0300
> From: "Andrey V. Golovin" <golovin at belozersky.msu.ru>
> Subject: [gmx-users] mopac gcc g77 and x86_64
> To: gmx-users at gromacs.org
> Message-ID: <47270306.6000607 at belozersky.msu.ru>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all,
> I faced with common problem I think :)
> Linux 64 bit, gcc and etc.
> I can't link libmopac.a from
> http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/
> qmmm.html
> because last one is 32 ...
> Building my own one with g77 or gfortran or f2c gives the same error
>
> cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
> -funroll-all-loops -o mdrun glaasje.o gctio.o init_sh.o ionize.o
> do_gct.o relax_sh.o repl_ex.o xutils.o compute_io.o md.o mdrun.o
> genalg.o -L/home/user/tmp/gromacs-3.3.2 -L/home/files/progs/fftw/lib
> ../mdlib/.libs/libmd_d.a ../gmxlib/.libs/libgmx_d.a -lnsl
> /home/files/progs/fftw/lib/libfftw3.a -lm -lmopac7 -lSM -lICE -lX11
> /home/user/tmp/gromacs-3.3.2/libmopac7.a(gmxmop.o): In function
> `moldat_':
> /home/user/tmp/mopac-sf/mopac7-1.10/src/gmxmop.c:1165: undefined
> reference to `i_indx'
> /home/user/tmp/mopac-sf/mopac7-1.10/src/gmxmop.c:1166: undefined
> reference to `i_indx'
> /home/user/tmp/mopac-sf/mopac7-1.10/src/gmxmop.c:1167: undefined
> reference to `i_indx'
> /home/user/tmp/mopac-sf/mopac7-1.10/src/gmxmop.c:1168: undefined
> reference to `i_indx'
> /home/user/tmp/mopac-sf/mopac7-1.10/src/gmxmop.c:1169: undefined
> reference to `i_indx'
> OR
> cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
> -funroll-all-loops -o mdrun glaasje.o gctio.o init_sh.o ionize.o
> do_gct.o relax_sh.o repl_ex.o xutils.o compute_io.o md.o mdrun.o
> genalg.o -L/home/user/tmp/gromacs-3.3.2 -L/home/files/progs/fftw/lib
> ../mdlib/.libs/libmd_d.a ../gmxlib/.libs/libgmx_d.a -lnsl
> /home/files/progs/fftw/lib/libfftw3.a -lm -lmopac7 -lSM -lICE -lX11
> /home/user/tmp/gromacs-3.3.2/libmopac7.a(gmxmop.o): In function
> `domop_':
> gmxmop.f:(.text+0x81): undefined reference to `_gfortran_string_index'
> /home/user/tmp/gromacs-3.3.2/libmopac7.a(gmxmop.o): In function
> `moldat_':
> gmxmop.f:(.text+0x2b8): undefined reference to `_gfortran_string_index'
> gmxmop.f:(.text+0x2d4): undefined reference to `_gfortran_string_index'
>
> and so on like no references defined at all.
>
> Looks like something stupid here... Any idea?
>
> PS Compiling mopac lib goes with some warnings but no errors.
>
> --
> -----------------------------------------------------------------
> Andrey V. Golovin
> Ph.D,Assistant Professor tel: (495) 939-3149
> Bioengineering and
> Bioinformatics Department
> Moscow State University fax: (495) 939-3181
> 119899 Moscow E-mail: golovin at genebee.msu.su
> Russia web: http://rnp-group.genebee.msu.su
> -----------------------------------------------------------------
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 30 Oct 2007 15:18:14 +0100
> From: tangxuan <tangxuan82 at gmail.com>
> Subject: Re: [gmx-users] g_sas problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1193753894.11293.13.camel at localhost.localdomain>
> Content-Type: text/plain
>
> Yes, the default value of -pbc is 'yes'. I did not add it in my
> command,
> but i think pbc should has been considered. It seems there is no
> contact between the two subunits, but at some specific time the total
> ASA of interaction region is very high(shown below).
>
> time total SAS of interaction region
> 15936 1.16099999999997
> 15937 1.09100000000004
> 15938 86.954
> 15939 1.16899999999998
> 15940 1.096
> 15941 1.22199999999998
> 15942 1.36900000000003
> 15943 89.423
> 15944 1.328
> 15945 91.182
> 15946 88.058
> 15947 1.33000000000001
> 15948 1.154
> 15949 1.21799999999996
> 15950 89.782
> 15951 89.541
> 15952 89.549
> 15953 89.691
> 15954 89.975
> 15955 89.018
> 15956 88.774
> 15957 88.46
> 15958 88.859
> 15959 89.69
> 15960 1.18900000000002
> 15961 88.087
> 15962 89.248
> 15963 89.78
> 15964 88.64
> 15965 90.222
> 15966 1.262
> 15967 1.23500000000001
> 15968 1.3290000000000
>
> Thanks for your help.
>
> Tang jiaowei
> On Tue, 2007-10-30 at 14:57 +0100, David van der Spoel wrote:
>> tangxuan wrote:
>>> Dear,all
>>> When I calculate the accessible surface area(ASA) of interaction
>>> region
>>> between two subunits A and B in my protein. First I calculated the
>>> ASA
>>> of A and B by "g_sas -f .xtc -s .tpr -n index.ndx -o .xvg -n
>>> index.ndx"
>>> respectively. After that, I combined A and B as the one group, then I
>>> computed SAS of group A+B in the same way above. When I calculated
>>> the
>>> hydrophobic SAS of interaction region between A and B by formula
>>> (SAS=SAS(A)+SAS(B)-SAS(A+B)), at some specific time this result is
>>> negative(the third ps in the result below). But in my opinion, this
>>> area
>>> should be positive. What is wrong? I can show you the result of the
>>> first 3 ps.
>>> A:
>>> 0 136.923 81.5686 218.491 0
>>> 1 136.149 87.5994 223.748 0
>>> 2 136.607 90.9957 227.603 0
>>> B:
>>> 0 129.967 85.1524 215.119 0
>>> 1 140.375 86.953 227.328 0
>>> 2 138.37 90.9806 229.35 0
>>> A+B:
>>> 0 264.215 169.394 433.608 0
>>> 1 274.129 176.945 451.074 0
>>> 2 276.924 180.027 456.951 0
>>>
>>> Look forward to your explanation.
>>
>> Hi Tang,
>>
>> I think this is actually a roundoff problem. It looks like your
>> proteins
>> make no contact at all. Did you use the -pbc flag (it may be default
>> though)
>>
>>>
>>> Thank you,
>>>
>>> Tang Jiaowei
>>>
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>
>
>
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> End of gmx-users Digest, Vol 42, Issue 102
> ******************************************
>
--
Gerrit Groenhof
MPI for Biophysical Chemistry
Am Fassberg 11
D-37077 Goettingen
Germany
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