[gmx-users] weird behavior of genion in gromacs4
Serena Leone
sleone at rics.bwh.harvard.edu
Thu Nov 6 23:44:49 CET 2008
Hi all
I'm trying for the first time to use the opls aa in gromacs4. When I
tried to use genion (my peptide has charge +7) I had the following
problem:
genion -s H1_em.tpr -conc 0.1 -neutral -nname opls_401 -pname opls_407
-p H1_opls.top -o H1_ions.gro
[...]
Reading file H1_em.tpr, VERSION 4.0 (single precision)
Using a coulomb cut-off of 1 nm
Will try to add 37 opls_407 ions and 44 opls_401 ions.
Select a continuous group of solvent molecules
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 ( System) has 61293 elements
Group 1 ( Protein) has 438 elements
Group 2 ( Protein-H) has 205 elements
Group 3 ( C-alpha) has 30 elements
Group 4 ( Backbone) has 90 elements
Group 5 ( MainChain) has 121 elements
Group 6 (MainChain+Cb) has 148 elements
Group 7 ( MainChain+H) has 147 elements
Group 8 ( SideChain) has 291 elements
Group 9 ( SideChain-H) has 84 elements
Group 10 ( Prot-Masses) has 438 elements
Group 11 ( Non-Protein) has 60855 elements
Group 12 ( SOL) has 60855 elements
Group 13 ( Other) has 60855 elements
Select a group: 12
Selected 12: 'SOL'
Number of (3-atomic) solvent molecules: 20285
Processing topology
Replacing 20204 solute molecules in topology file (H1_opls.top) by 37
opls_407 and 44 opls_401 ions.
Back Off! I just backed up H1_opls.top to ./#H1_opls.top.2#
Replacing solvent molecule 2379 (atom 7575) with opls_401
Replacing solvent molecule 15369 (atom 46545) with opls_401
Replacing solvent molecule 9901 (atom 30141) with opls_401
Replacing solvent molecule 17162 (atom 51924) with opls_401
Replacing solvent molecule 6755 (atom 20703) with opls_401
Replacing solvent molecule 3249 (atom 10185) with opls_401
Replacing solvent molecule 7832 (atom 23934) with opls_401
Replacing solvent molecule 17973 (atom 54357) with opls_407
Replacing solvent molecule 7991 (atom 24411) with opls_401
Replacing solvent molecule 13300 (atom 40338) with opls_407
Replacing solvent molecule 10849 (atom 32985) with opls_401
Replacing solvent molecule 14409 (atom 43665) with opls_407
Replacing solvent molecule 8234 (atom 25140) with opls_401
Replacing solvent molecule 7949 (atom 24285) with opls_407
Replacing solvent molecule 6055 (atom 18603) with opls_401
Replacing solvent molecule 1658 (atom 5412) with opls_407
Replacing solvent molecule 5699 (atom 17535) with opls_401
Replacing solvent molecule 10311 (atom 31371) with opls_407
Replacing solvent molecule 8324 (atom 25410) with opls_401
Replacing solvent molecule 2879 (atom 9075) with opls_407
Replacing solvent molecule 3883 (atom 12087) with opls_401
Replacing solvent molecule 4025 (atom 12513) with opls_407
Replacing solvent molecule 4130 (atom 12828) with opls_401
Replacing solvent molecule 11561 (atom 35121) with opls_407
Replacing solvent molecule 12507 (atom 37959) with opls_401
Replacing solvent molecule 16316 (atom 49386) with opls_407
Replacing solvent molecule 2297 (atom 7329) with opls_401
Replacing solvent molecule 1062 (atom 3624) with opls_407
Replacing solvent molecule 10975 (atom 33363) with opls_401
Replacing solvent molecule 14257 (atom 43209) with opls_407
Replacing solvent molecule 8337 (atom 25449) with opls_401
Replacing solvent molecule 4583 (atom 14187) with opls_407
Replacing solvent molecule 3348 (atom 10482) with opls_401
Replacing solvent molecule 11039 (atom 33555) with opls_407
Replacing solvent molecule 18891 (atom 57111) with opls_401
Replacing solvent molecule 1053 (atom 3597) with opls_407
Replacing solvent molecule 5821 (atom 17901) with opls_401
Replacing solvent molecule 4102 (atom 12744) with opls_407
Replacing solvent molecule 7098 (atom 21732) with opls_401
Replacing solvent molecule 7756 (atom 23706) with opls_407
Replacing solvent molecule 6442 (atom 19764) with opls_401
Replacing solvent molecule 12107 (atom 36759) with opls_407
Replacing solvent molecule 7594 (atom 23220) with opls_401
Replacing solvent molecule 5653 (atom 17397) with opls_407
Replacing solvent molecule 13928 (atom 42222) with opls_401
Replacing solvent molecule 124 (atom 810) with opls_407
Replacing solvent molecule 8965 (atom 27333) with opls_401
Replacing solvent molecule 497 (atom 1929) with opls_407
Replacing solvent molecule 16943 (atom 51267) with opls_401
Replacing solvent molecule 18565 (atom 56133) with opls_407
Replacing solvent molecule 14513 (atom 43977) with opls_401
Replacing solvent molecule 10901 (atom 33141) with opls_407
Replacing solvent molecule 2568 (atom 8142) with opls_401
Replacing solvent molecule 369 (atom 1545) with opls_407
Replacing solvent molecule 5572 (atom 17154) with opls_401
Replacing solvent molecule 1125 (atom 3813) with opls_407
Replacing solvent molecule 5241 (atom 16161) with opls_401
Replacing solvent molecule 5544 (atom 17070) with opls_407
Replacing solvent molecule 13953 (atom 42297) with opls_401
Replacing solvent molecule 11866 (atom 36036) with opls_407
Replacing solvent molecule 17697 (atom 53529) with opls_401
Replacing solvent molecule 17939 (atom 54255) with opls_407
Replacing solvent molecule 5987 (atom 18399) with opls_401
Replacing solvent molecule 3749 (atom 11685) with opls_407
Replacing solvent molecule 18189 (atom 55005) with opls_401
Replacing solvent molecule 2572 (atom 8154) with opls_407
Replacing solvent molecule 9856 (atom 30006) with opls_401
Replacing solvent molecule 11617 (atom 35289) with opls_407
Replacing solvent molecule 8105 (atom 24753) with opls_401
Replacing solvent molecule 16434 (atom 49740) with opls_407
Replacing solvent molecule 6677 (atom 20469) with opls_401
Replacing solvent molecule 13865 (atom 42033) with opls_407
Replacing solvent molecule 737 (atom 2649) with opls_401
Replacing solvent molecule 15670 (atom 47448) with opls_407
Replacing solvent molecule 9657 (atom 29409) with opls_401
Replacing solvent molecule 10953 (atom 33297) with opls_407
Replacing solvent molecule 13138 (atom 39852) with opls_401
Replacing solvent molecule 5968 (atom 18342) with opls_407
Replacing solvent molecule 12065 (atom 36633) with opls_401
Replacing solvent molecule 7500 (atom 22938) with opls_407
Replacing solvent molecule 2006 (atom 6456) with opls_401
*** buffer overflow detected ***: genion terminated
======= Backtrace: =========
/lib/libc.so.6(__fortify_fail+0x37)[0x7f0d4a5cf887]
/lib/libc.so.6[0x7f0d4a5cd750]
/usr/local/gromacs/lib/libgmx.so.5(write_hconf_indexed_p+0x7e4)[0x7f0d4afd27f4]
/usr/local/gromacs/lib/libgmx.so.5(write_hconf_p+0xf6)[0x7f0d4afd2916]
/usr/local/gromacs/lib/libgmx.so.5(write_conf_p+0x64)[0x7f0d4afd29c4]
/usr/local/gromacs/lib/libgmx.so.5(write_sto_conf+0x10f)[0x7f0d4afd3d2f]
/usr/local/gromacs/lib/libgmxana.so.5(gmx_genion+0xf30)[0x7f0d4b8efb70]
/lib/libc.so.6(__libc_start_main+0xe6)[0x7f0d4a4ee466]
genion[0x4005b9]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:06 9838982
/usr/local/gromacs/bin/genion
00600000-00601000 r--p 00000000 08:06 9838982
/usr/local/gromacs/bin/genion
00601000-00602000 rw-p 00001000 08:06 9838982
/usr/local/gromacs/bin/genion
018af000-01e69000 rw-p 018af000 00:00 0
[heap]
7f0d49793000-7f0d497a9000 r-xp 00000000 08:06 4423691
/lib/libgcc_s.so.1
7f0d497a9000-7f0d499a9000 ---p 00016000 08:06 4423691
/lib/libgcc_s.so.1
7f0d499a9000-7f0d499aa000 r--p 00016000 08:06 4423691
/lib/libgcc_s.so.1
7f0d499aa000-7f0d499ab000 rw-p 00017000 08:06 4423691
/lib/libgcc_s.so.1
7f0d499be000-7f0d49dd0000 rw-p 7f0d499be000 00:00 0
7f0d49dd8000-7f0d49f40000 rw-p 7f0d49dd8000 00:00 0
7f0d49f7c000-7f0d4a14c000 rw-p 7f0d49f7c000 00:00 0
7f0d4a200000-7f0d4a2b4000 rw-p 7f0d4a200000 00:00 0
7f0d4a2b4000-7f0d4a2cb000 r-xp 00000000 08:06 4424289
/lib/libpthread-2.8.90.so
7f0d4a2cb000-7f0d4a4ca000 ---p 00017000 08:06 4424289
/lib/libpthread-2.8.90.so
7f0d4a4ca000-7f0d4a4cb000 r--p 00016000 08:06 4424289
/lib/libpthread-2.8.90.so
7f0d4a4cb000-7f0d4a4cc000 rw-p 00017000 08:06 4424289
/lib/libpthread-2.8.90.so
7f0d4a4cc000-7f0d4a4d0000 rw-p 7f0d4a4cc000 00:00 0
7f0d4a4d0000-7f0d4a639000 r-xp 00000000 08:06 4424275
/lib/libc-2.8.90.so
7f0d4a639000-7f0d4a838000 ---p 00169000 08:06 4424275
/lib/libc-2.8.90.so
7f0d4a838000-7f0d4a83c000 r--p 00168000 08:06 4424275
/lib/libc-2.8.90.so
7f0d4a83c000-7f0d4a83d000 rw-p 0016c000 08:06 4424275
/lib/libc-2.8.90.so
7f0d4a83d000-7f0d4a842000 rw-p 7f0d4a83d000 00:00 0
7f0d4a842000-7f0d4a8c6000 r-xp 00000000 08:06 4424279
/lib/libm-2.8.90.so
7f0d4a8c6000-7f0d4aac5000 ---p 00084000 08:06 4424279
/lib/libm-2.8.90.so
7f0d4aac5000-7f0d4aac6000 r--p 00083000 08:06 4424279
/lib/libm-2.8.90.so
7f0d4aac6000-7f0d4aac7000 rw-p 00084000 08:06 4424279
/lib/libm-2.8.90.so
7f0d4aac7000-7f0d4ab7a000 r-xp 00000000 08:06 9504361
/usr/lib/libfftw3f.so.3.1.2
7f0d4ab7a000-7f0d4ad79000 ---p 000b3000 08:06 9504361
/usr/lib/libfftw3f.so.3.1.2
7f0d4ad79000-7f0d4ad7f000 r--p 000b2000 08:06 9504361
/usr/lib/libfftw3f.so.3.1.2
7f0d4ad7f000-7f0d4ad80000 rw-p 000b8000 08:06 9504361
/usr/lib/libfftw3f.so.3.1.2
7f0d4ad80000-7f0d4ad96000 r-xp 00000000 08:06 4424281
/lib/libnsl-2.8.90.so
7f0d4ad96000-7f0d4af95000 ---p 00016000 08:06 4424281
/lib/libnsl-2.8.90.so
7f0d4af95000-7f0d4af96000 r--p 00015000 08:06 4424281
/lib/libnsl-2.8.90.so
7f0d4af96000-7f0d4af97000 rw-p 00016000 08:06 4424281
/lib/libnsl-2.8.90.so
7f0d4af97000-7f0d4af99000 rw-p 7f0d4af97000 00:00 0
7f0d4af99000-7f0d4b26c000 r-xp 00000000 08:06 9838943
/usr/local/gromacs/lib/libgmx.so.5.0.0
7f0d4b26c000-7f0d4b46c000 ---p 002d3000 08:06 9838943
/usr/local/gromacs/lib/libgmx.so.5.0.0
7f0d4b46c000-7f0d4b470000 r--p 002d3000 08:06 9838943
/usr/local/gromacs/lib/libgmx.so.5.0.0
7f0d4b470000-7f0d4b478000 rw-p 002d7000 08:06 9838943
/usr/local/gromacs/lib/libgmx.so.5.0.0
7f0d4b478000-7f0d4b47e000 rw-p 7f0d4b478000 00:00 0
7f0d4b47e000-7f0d4b58a000 r-xp 00000000 08:06 9838947
/usr/local/gromacs/lib/libmd.so.5.0.0
7f0d4b58a000-7f0d4b789000 ---p 0010c000 08:06 9838947
/usr/local/gromacs/lib/libmd.so.5.0.0
7f0d4b789000-7f0d4b78a000 r--p 0010b000 08:06 9838947
/usr/local/gromacs/lib/libmd.so.5.0.0
7f0d4b78a000-7f0d4b78c000 rw-p 0010c000 08:06 9838947
/usr/local/gromacs/lib/libmd.so.5.0.0
7f0d4b78c000-7f0d4b93d000 r-xp 00000000 08:06 9838963
/usr/local/gromacs/lib/libgmxana.so.5.0.0
7f0d4b93d000-7f0d4bb3d000 ---p 001b1000 08:06 9838963
/usr/local/gromacs/lib/libgmxana.so.5.0.0
7f0d4bb3d000-7f0d4bb3e000 r--p 001b1000 08:06 9838963
/usr/local/gromacs/lib/libgmxana.so.5.0.0
7f0d4bb3e000-7f0d4bb44000 rw-p 001b2000 08:06 9838963
/usr/local/gromacs/lib/libgmxana.so.5.0.0
7f0d4bb44000-7f0d4bb46000 rw-p 7f0d4bb44000 00:00 0
7f0d4bb46000-7f0d4bb65000 r-xp 00000000 08:06 4423748
/lib/ld-2.8.90.so
7f0d4bba6000-7f0d4bd4d000 rw-p 7f0d4bba6000 00:00 0
7f0d4bd5d000-7f0d4bd64000 rw-p 7f0d4bd5d000 00:00 0
7f0d4bd64000-7f0d4bd65000 r--p 0001e000 08:06 4423748
/lib/ld-2.8.90.so
7f0d4bd65000-7f0d4bd66000 rw-p 0001f000 08:06 4423748
/lib/ld-2.8.90.so
7fff53d51000-7fff53d66000 rwxp 7ffffffea000 00:00 0
[stack]
7fff53dff000-7fff53e00000 r-xp 7fff53dff000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
Aborted
After this, the topology had the ions, but not the .gro
Does anybody knows what's wrong? It worked properly when I made a first
trial with gromos96...
Also, why does it want to "Replacing 20204 solute molecules in topology
file (H1_opls.top) by 37 opls_407 and 44 opls_401 ions"?
Thank you very much
Serena
--
Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel) 617-732-8586
The information transmitted in this electronic communication is intended only
for the person or entity to whom it is addressed and may contain confidential
and/or privileged material. Any review, retransmission, dissemination or other
use of or taking of any action in reliance upon this information by persons or
entities other than the intended recipient is prohibited. If you received this
information in error, please contact the Compliance HelpLine at 800-856-1983 and
properly dispose of this information.
More information about the gromacs.org_gmx-users
mailing list