[gmx-users] converting .xpm to .eps

[Nidhi Jatana]

Dear Sir/Madam
Please find attached the file containing the error.

Thanking you

Regards
-- 
Nidhi Jatana
Senior Research Fellow
Bioinformatics Center
Sri Venkateswara College
(University of Delhi)
Dhaula Kuan
New Delhi-110021.



On Thu, Dec 19, 2013 at 7:44 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:

> On 12/19/2013 12:53 PM, Nidhi Jatana wrote:
>
>> Dear Sir/Madam
>> I generated the atomic density plot using g_densmap by giving the
>> following
>> command:
>> g_densmap -f *.xtc -s *.pdb -n *.ndx -o *.xpm
>>
>> The calculation completed successfully but when I am trying to convert
>> .xpm
>> file to .eps file using xpm2ps command, its giving error and aborts.
>>
> What is the error message?
>
> If I use your set of commands with Gromacs 4.6.4, I can successfully create
> an EPS file.
>
> Carsten
>
>
>> xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm
>>
>> I have tried many options with setting -bx and -by but of no help. I also
>> tried taking the .m2p file but the problem persist. Please find attached
>> the .m2p file for reference. Please help me with this.
>>
>> Thanking you
>>
>> Regards
>>   --
>> Nidhi Jatana
>> Senior Research Fellow
>> Bioinformatics Center
>> Sri Venkateswara College
>> (University of Delhi)
>> Dhaula Kuan
>> New Delhi-110021.
>>
>>
>>
> --
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-------------- next part --------------
There is 1 matrix in densmap_drd4_wild_dop_binding.xpm
Matrix 0 is 335 x 419
Auto tick spacing failed for X-axis, guessing 0.199793
Auto tick spacing for X-axis: major 0.199793, minor 0.0399586
Auto tick spacing failed for Y-axis, guessing 0.200196
Auto tick spacing for Y-axis: major 0.200196, minor 0.0400392
Set the x-size of the box to 1.194
Set the y-size of the box to 1.194

Back Off! I just backed up plot_wild_dop_binding.eps to ./#plot_wild_dop_binding.eps.2#
*** buffer overflow detected ***: xpm2ps terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7fc119e15f6c]
/lib/x86_64-linux-gnu/libc.so.6(+0x109e40)[0x7fc119e14e40]
/usr/local/gromacs/bin/../lib/libgmxana.so.6(ps_mat+0x101e)[0x7fc11a49aa6e]
/usr/local/gromacs/bin/../lib/libgmxana.so.6(do_mat+0x61f)[0x7fc11a49ea7f]
/usr/local/gromacs/bin/../lib/libgmxana.so.6(gmx_xpm2ps+0x1137)[0x7fc11a4a10a7]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fc119d2c76d]
xpm2ps[0x400761]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:01 18613233                           /usr/local/gromacs/bin/xpm2ps
00600000-00601000 r--p 00000000 08:01 18613233                           /usr/local/gromacs/bin/xpm2ps
00601000-00602000 rw-p 00001000 08:01 18613233                           /usr/local/gromacs/bin/xpm2ps
02150000-021b3000 rw-p 00000000 00:00 0                                  [heap]
7fc117dde000-7fc117df3000 r-xp 00000000 08:01 38538696                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fc117df3000-7fc117ff2000 ---p 00015000 08:01 38538696                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fc117ff2000-7fc117ff3000 r--p 00014000 08:01 38538696                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fc117ff3000-7fc117ff4000 rw-p 00015000 08:01 38538696                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fc117ff4000-7fc117ff7000 rw-p 00000000 00:00 0 
7fc117ff7000-7fc117ffe000 r-xp 00000000 08:01 38539610                   /lib/x86_64-linux-gnu/librt-2.15.so
7fc117ffe000-7fc1181fd000 ---p 00007000 08:01 38539610                   /lib/x86_64-linux-gnu/librt-2.15.so
7fc1181fd000-7fc1181fe000 r--p 00006000 08:01 38539610                   /lib/x86_64-linux-gnu/librt-2.15.so
7fc1181fe000-7fc1181ff000 rw-p 00007000 08:01 38539610                   /lib/x86_64-linux-gnu/librt-2.15.so
7fc1181ff000-7fc118200000 rw-p 00000000 00:00 0 
7fc118200000-7fc118202000 r-xp 00000000 08:01 38539621                   /lib/x86_64-linux-gnu/libdl-2.15.so
7fc118202000-7fc118402000 ---p 00002000 08:01 38539621                   /lib/x86_64-linux-gnu/libdl-2.15.so
7fc118402000-7fc118403000 r--p 00002000 08:01 38539621                   /lib/x86_64-linux-gnu/libdl-2.15.so
7fc118403000-7fc118404000 rw-p 00003000 08:01 38539621                   /lib/x86_64-linux-gnu/libdl-2.15.so
7fc118404000-7fc1184a3000 r-xp 00000000 08:01 13899638                   /usr/lib/libblas/libblas.so.3.0
7fc1184a3000-7fc1186a2000 ---p 0009f000 08:01 13899638                   /usr/lib/libblas/libblas.so.3.0
7fc1186a2000-7fc1186a3000 r--p 0009e000 08:01 13899638                   /usr/lib/libblas/libblas.so.3.0
7fc1186a3000-7fc1186a4000 rw-p 0009f000 08:01 13899638                   /usr/lib/libblas/libblas.so.3.0
7fc1186a4000-7fc11880b000 r-xp 00000000 08:01 14553690                   /usr/local/lib/libfftw3f.so.3.3.2
7fc11880b000-7fc118a0a000 ---p 00167000 08:01 14553690                   /usr/local/lib/libfftw3f.so.3.3.2
7fc118a0a000-7fc118a16000 r--p 00166000 08:01 14553690                   /usr/local/lib/libfftw3f.so.3.3.2
7fc118a16000-7fc118a17000 rw-p 00172000 08:01 14553690                   /usr/local/lib/libfftw3f.so.3.3.2
7fc118a17000-7fc118a18000 rw-p 00000000 00:00 0 
7fc118a18000-7fc118a26000 r-xp 00000000 08:01 13901086                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fc118a26000-7fc118c25000 ---p 0000e000 08:01 13901086                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fc118c25000-7fc118c26000 r--p 0000d000 08:01 13901086                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fc118c26000-7fc118c27000 rw-p 0000e000 08:01 13901086                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fc118c27000-7fc118d22000 r-xp 00000000 08:01 38539619                   /lib/x86_64-linux-gnu/libm-2.15.so
7fc118d22000-7fc118f21000 ---p 000fb000 08:01 38539619                   /lib/x86_64-linux-gnu/libm-2.15.so
7fc118f21000-7fc118f22000 r--p 000fa000 08:01 38539619                   /lib/x86_64-linux-gnu/libm-2.15.so
7fc118f22000-7fc118f23000 rw-p 000fb000 08:01 38539619                   /lib/x86_64-linux-gnu/libm-2.15.so
7fc118f23000-7fc119527000 r-xp 00000000 08:01 18613177                   /usr/local/gromacs/lib/libgmx.so.6
7fc119527000-7fc119726000 ---p 00604000 08:01 18613177                   /usr/local/gromacs/lib/libgmx.so.6
7fc119726000-7fc11972c000 r--p 00603000 08:01 18613177                   /usr/local/gromacs/lib/libgmx.so.6
7fc11972c000-7fc119741000 rw-p 00609000 08:01 18613177                   /usr/local/gromacs/lib/libgmx.so.6
7fc119741000-7fc119742000 rw-p 00000000 00:00 0 
7fc119742000-7fc119b08000 r-xp 00000000 08:01 18613181                   /usr/local/gromacs/lib/libmd.so.6
7fc119b08000-7fc119d08000 ---p 003c6000 08:01 18613181                   /usr/local/gromacs/lib/libmd.so.6
7fc119d08000-7fc119d09000 r--p 003c6000 08:01 18613181                   /usr/local/gromacs/lib/libmd.so.6
7fc119d09000-7fc119d0b000 rw-p 003c7000 08:01 18613181                   /usr/local/gromacs/lib/libmd.so.6
7fc119d0b000-7fc119ec0000 r-xp 00000000 08:01 38539623                   /lib/x86_64-linux-gnu/libc-2.15.so
7fc119ec0000-7fc11a0c0000 ---p 001b5000 08:01 38539623                   /lib/x86_64-linux-gnu/libc-2.15.so
7fc11a0c0000-7fc11a0c4000 r--p 001b5000 08:01 38539623                   /lib/x86_64-linux-gnu/libc-2.15.so
7fc11a0c4000-7fc11a0c6000 rw-p 001b9000 08:01 38539623                   /lib/x86_64-linux-gnu/libc-2.15.so
7fc11a0c6000-7fc11a0cb000 rw-p 00000000 00:00 0 
7fc11a0cb000-7fc11a0e3000 r-xp 00000000 08:01 38539606                   /lib/x86_64-linux-gnu/libpthread-2.15.so
7fc11a0e3000-7fc11a2e2000 ---p 00018000 08:01 38539606                   /lib/x86_64-linux-gnu/libpthread-2.15.so
7fc11a2e2000-7fc11a2e3000 r--p 00017000 08:01 38539606                   /lib/x86_64-linux-gnu/libpthread-2.15.so
7fc11a2e3000-7fc11a2e4000 rw-p 00018000 08:01 38539606                   /lib/x86_64-linux-gnu/libpthread-2.15.so
7fc11a2e4000-7fc11a2e8000 rw-p 00000000 00:00 0 
7fc11a2e8000-7fc11a56f000 r-xp 00000000 08:01 18613377                   /usr/local/gromacs/lib/libgmxana.so.6
7fc11a56f000-7fc11a76f000 ---p 00287000 08:01 18613377                   /usr/local/gromacs/lib/libgmxana.so.6
7fc11a76f000-7fc11a770000 r--p 00287000 08:01 18613377                   /usr/local/gromacs/lib/libgmxana.so.6
7fc11a770000-7fc11a77d000 rw-p 00288000 08:01 18613377                   /usr/local/gromacs/lib/libgmxana.so.6
7fc11a77d000-7fc11a77f000 rw-p 00000000 00:00 0 
7fc11a77f000-7fc11a7a1000 r-xp 00000000 08:01 38539611                   /lib/x86_64-linux-gnu/ld-2.15.so
7fc11a97d000-7fc11a97f000 rw-p 00000000 00:00 0 
7fc11a99c000-7fc11a9a1000 rw-p 00000000 00:00 0 
7fc11a9a1000-7fc11a9a2000 r--p 00022000 08:01 38539611                   /lib/x86_64-linux-gnu/ld-2.15.so
7fc11a9a2000-7fc11a9a4000 rw-p 00023000 08:01 38539611                   /lib/x86_64-linux-gnu/ld-2.15.so
7fff643e9000-7fff6440a000 rw-p 00000000 00:00 0                          [stack]
7fff6446b000-7fff6446c000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted