[gmx-users] Re: mopac gcc g77 and x86_64
Andrey V. Golovin
golovin at belozersky.msu.ru
Tue Oct 30 13:51:38 CET 2007
Gerrit Groenhof wrote:
Dear Gerrit,
Thanx it's works ! it was really silly ...
Is pcgamess interface expected in future? I saw some traces in list that
it could be ...
Andrey
> 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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--
-----------------------------------------------------------------
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
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