i want to generate parameters for methane, but i am facing some problem
antechamber -i meth.pdb -fi pdb -o meth.mol2 -fo mol2 -c bcc
parmchk2 -i meth.mol2 -f mol2 -o meth.frcmod
tleap
source leaprc.gaff
unk = loadmol2 meth.mol2
check unk
saveoff unk meth.lib
quit
tleap
source leaprc.gaff
loadamberparams meth.frcmod
loadoff meth.lib
source leaprc.ff14SB
source leaprc.tip3p
a = loadpdb meth.pdb (here meth.pdb contains 0.1M cocn of methane and water
also )
set a box {88 88 88}
check a
saveamberparm a a.prmtop a.inpcrd
Till here everything is okay. but when i submit my job i got the following
error
[warn] Epoll ADD(4) on fd 1 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
[warn] Epoll ADD(4) on fd 2 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
[compute12:26682:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
2 0x000000000006749c mxm_handle_error()
/var/tmp/OFED_topdir/BUILD/mxm-3.5.3092/src/mxm/util/debug/debug.c:641
3 0x00000000000679ec mxm_error_signal_handler()
/var/tmp/OFED_topdir/BUILD/mxm-3.5.3092/src/mxm/util/debug/debug.c:616
4 0x0000000000035670 killpg() ??:0
5 0x000000000048f198 __pme_slab_recip_mod_MOD_do_slab_pmesh_kspace() ??:0
6 0x00000000004aef3d __pme_force_mod_MOD_pme_force() ??:0
7 0x00000000004e686a __runmin_mod_MOD_runmin_slave() ??:0
8 0x000000000051291c MAIN__() pmemd.F90:0
9 0x000000000040cc0d main() ??:0
10 0x0000000000021b15 __libc_start_main() ??:0
11 0x000000000040d0b9 _start() ??:0
===================
[warn] Epoll ADD(4) on fd 1 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
[warn] Epoll ADD(4) on fd 2 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
At line 566 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.in')
Fortran runtime error: End of file
[warn] Epoll ADD(4) on fd 1 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
[warn] Epoll ADD(4) on fd 2 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
Unit 9 Error on OPEN: heat.rst
[warn] Epoll ADD(4) on fd 1 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
[warn] Epoll ADD(4) on fd 2 failed. Old events were 0; read change was 0
(none); write change was 1 (add): Operation not permitted
Unit 9 Error on OPEN: eq.rst
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Received on Fri Jun 26 2020 - 00:30:04 PDT
