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" <[EMAIL PROTECTED]>
Subject: [gmx-users] mopac gcc g77 and x86_64
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
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: [EMAIL PROTECTED]
Russia web: http://rnp-group.genebee.msu.su
-----------------------------------------------------------------
------------------------------
Message: 7
Date: Tue, 30 Oct 2007 15:18:14 +0100
From: tangxuan <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] g_sas problem
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
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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