[gmx-users] weird behavior of genion in gromacs4
Justin A. Lemkul
jalemkul at vt.edu
Thu Nov 6 23:56:48 CET 2008
Serena Leone wrote:
> 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
>
You should probably try specifying the atom names of those ions (NA+ and CL-, as
shown in ions.itp), instead of their atom types.
-Justin
> [...]
> 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
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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