[gmx-users] grompp errors

[Amanda Watkins]

Tue, July 13, 2010 11:46:58 AM
grompp errors...
From: Amanda Watkins <mhstrumpetgirl at yahoo.com> ...View Contact 
To: gmx-users at gromacs.org  
________________________________

Dear GROMACS users,

I am trying to simulate a protein  (OmpA) and a detergent (DPC) together in 
GROMACS. I have successfully  generate and minimized the protein and the 
detergent separately and now I  have inserted 216 DPC molecules into the protein 
box, and whenever I  try to upload them with grompp for mdrun, I get this 
message:

Ignoring  obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing  old mdp entry 'unconstrained_start' by 'continuation'

Back Off! I  just backed up mdout.mdp to ./#mdout.mdp.18#
checking input for  internal consistency...

NOTE 1 [file em.mdp, line unknown]:
   For energy conservation with switch/shift potentials, rlist should be  0.1
  to 0.3 nm larger than rcoulomb.


NOTE 2 [file em.mdp,  line  unknown]:
  For energy conservation with switch/shift potentials,  rlist should be 0.1
  to 0.3 nm larger than rvdw.

processing  topology...
Opening library file /usr/share/gromacs/top/ffG53a6.itp
Opening  library file /usr/share/gromacs/top/ffG53a6nb.itp
Opening library  file /usr/share/gromacs/top/ffG53a6bon.itp
Opening library file  /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596  non-bonded parameter combinations
Opening library file  /usr/share/gromacs/top/spc.itp
Opening library file  /usr/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours  molecule type 'Protein_A'
Excluding 3 bonded neighbours molecule type  'DPC'

NOTE 3 [file 1qjp.top, line 8723]:
  System has  non-zero total charge: -1.000001e+00
  


processing  coordinates...
double-checking input for internal consistency...
renumbering  atomtypes...
converting bonded parameters...

ERROR 1  [file 1qjp.top, line 8723]:
  atom NC3 (Res DPC-1) has mass 0



ERROR  2 [file 1qjp.top, line 8723]:
  atom PO4 (Res DPC-1) has mass 0



ERROR  3 [file 1qjp.top, line 8723]:
  atom C1 (Res DPC-1) has mass 0



ERROR  4 [file 1qjp.top, line 8723]:
  atom C2 (Res DPC-1) has mass 0



ERROR  5 [file 1qjp.top, line 8723]:
  atom C3 (Res DPC-1) has mass 0



There  were 3 notes

-------------------------------------------------------
Program  grompp, VERSION 4.0.7
Source code file:  ../../../../src/kernel/grompp.c, line: 986

Fatal error:
There  were 5 errors in input file(s)
-------------------------------------------------------

"Take  Your Medications and Preparations and Ram It Up Your Snout" (F. Zappa)


*Here is the file that it is having trouble processing:

dpc1.itp:

; topology for a dodecylphosphocholine  lipid
    
[ moleculetype ]
; Name   nrexcl
DPC     3

[  atoms ]
;   nr    type   resnr  residu    atom    cgnr         charge          mass
     1      NL       1    DPC     NC3        1         0.0    ; qtot: 2.24
     2        P       1    DPC      PO4       1         0.0    ; qtot: 3.28
     3      CH2       1    DPC      C1       1         0.0    ; qtot: 1
      4     CH2       1    DPC      C2       1         0.0    ; qtot: 1
      5     CH3       1    DPC      C3       1         0.0    ; qtot: 3

Is there something that I am inputing wrong?  Or is it that I need to regenerate 
the DPC molecules to  include all of the atoms within the molecule? Whenever I 
tried to use the other .itp file it gives me the error that there is an atom 
difference. This new error is my attempt to fix this error.

Sincerely,

~Amanda  Watkins

SBC 2012


      
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