[gmx-users] problem regarding grompp

[kinshuk at chem.iitb.ac.in]

Hi all,
 I have been trying to simulate peptide (octa alanine). In genbox i have
inserted 40 molecule of guanidium ion & 800 water molecule (by -ci &
maxsol option in gromacs 3.3.3)then again with genbox i added 40
molecules of thiocynate ion & 80 water molecules as above mentioned way.
When i tried to do grompp for energy minimization i was encountered with
many warning listed below though i have included the *.itp files of both
ions in the topology *.top file of peptide.I need some insight about this
so that i can resolve this problem.

I have attached the em.mdp file along with this mail.

If i will be getting help i'll be thankful for you.

#THIS IS A GRO FILE OF SCN- ion (SCN)#

PRODRG COORDS
    3
    1SCN  N        1  -0.814   0.083   1.049
    1SCN  C        2  -0.768   0.080   1.153
    1SCN  S        3  -0.702   0.077   1.303
   0.40400   0.40400   0.40400

#This is a gro file of guanidium ion(GUD).#

PRODRG COORDS
   10
    1GUD  N1       1   2.240  -2.939  -6.422
    1GUD  HAA      2   2.152  -2.946  -6.376
    1GUD  HAB      3   2.242  -2.917  -6.520
    1GUD  C        4   2.353  -2.958  -6.355
    1GUD  N3       5   2.470  -2.948  -6.418
    1GUD  HAF      6   2.556  -2.962  -6.369
    1GUD  HAE      7   2.473  -2.926  -6.516
    1GUD  N2       8   2.350  -2.987  -6.225
    1GUD  HAD      9   2.435  -3.001  -6.175
    1GUD  HAC     10   2.262  -2.994  -6.178



The warning that i have encountered is like...



creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
checking input for internal consistency...
Note: Old option for temperature coupling given: changing "yes" to
"Berendsen"
ERROR: With coulombtype = PME, rcoulomb must be equal to rlist
calling /lib/cpp...
processing topology...
Generated 432 of the 1378 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 3 bonded neighbours for GUD 40
Excluding 3 bonded neighbours for SCN 40
Excluding 2 bonded neighbours for SOL 800
Excluding 2 bonded neighbours for SOL 88
processing coordinates...
Warning: atom names in t.top and after_sol.gro don't match (N - OW)
Warning: atom names in t.top and after_sol.gro don't match (C - HW1)
Warning: atom names in t.top and after_sol.gro don't match (S - HW2)
Warning: atom names in t.top and after_sol.gro don't match (N - OW)
Warning: atom names in t.top and after_sol.gro don't match (C - HW1)
Warning: atom names in t.top and after_sol.gro don't match (S - HW2)
Warning: atom names in t.top and after_sol.gro don't match (N - OW)
Warning: atom names in t.top and after_sol.gro don't match (C - HW1)
Warning: atom names in t.top and after_sol.gro don't match (S - HW2)
Warning: atom names in t.top and after_sol.gro don't match (N - OW)
Warning: atom names in t.top and after_sol.gro don't match (C - HW1)
Warning: atom names in t.top and after_sol.gro don't match (S - HW2)
Warning: atom names in t.top and after_sol.gro don't match (N - OW)
Warning: atom names in t.top and after_sol.gro don't match (C - HW1)
Warning: atom names in t.top and after_sol.gro don't match (S - HW2)
Warning: atom names in t.top and after_sol.gro don't match (N - OW)
Warning: atom names in t.top and after_sol.gro don't match (C - HW1)
Warning: atom names in t.top and after_sol.gro don't match (S - HW2)
Warning: atom names in t.top and after_sol.gro don't match (N - OW)
Warning: atom names in t.top and after_sol.gro don't match (C - HW1)
(more than 20 non-matching atom names)
WARNING 1 [file "t.top", line 405]:
  240 non-matching atom names
  atom names from t.top will be used
  atom names from after_sol.gro will be ignored

double-checking input for internal consistency...
There was 1 warning
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 1109

Fatal error:
There were 1 error(s) processing your input
-------------------------------------------------------

"Stop Drinking My Beer !" (The Amps)
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