Anil Kumar wrote:
Dear All,
Can anyone help me in running simulation in explicit urea.
When i was using urea+h2o.gro and urea.itp and tried to do simulation in
explicit urea.
After doing genbox, i am not able to do the grompp for energy minimization
and getting the error which is given below.
I have added masses of all the atoms of urea in atommass.dat file, but
still getting the same error.
This file isn't used for making topologies.
Please help me, where does am i making the mistakes.
processing coordinates...
Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)
Well, if these don't match you're doing something wrongly, but I can't
tell what.
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
# BONDS: 945
# G96BONDS: 128
# ANGLES: 1215
# G96ANGLES: 190
# PDIHS: 1134
# IDIHS: 485
# LJ14: 1242
# SETTLE: 2050
ERROR 4 [file "base.top", line 808]:
atom C1 (Res UREA-11) has mass 0
ERROR 5 [file "base.top", line 808]:
atom O2 (Res UREA-11) has mass 0
ERROR 6 [file "base.top", line 808]:
atom N3 (Res UREA-11) has mass 0
ERROR 7 [file "base.top", line 808]:
atom H4 (Res UREA-11) has mass 0
ERROR 8 [file "base.top", line 808]:
atom H5 (Res UREA-11) has mass 0
ERROR 9 [file "base.top", line 808]:
atom N6 (Res UREA-11) has mass 0
ERROR 10 [file "base.top", line 808]:
atom H7 (Res UREA-11) has mass 0
Your force field's .rtp file needs entries for these atoms, probably.
Mark
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