[gmx-users] tfe

[shahrbanoo karbalaee]

Dear justin
here it is.

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
WARNING 1 [file em.mdp, line unknown]:
  Unknown left-hand 'constrains' in parameter file

WARNING 2 [file em.mdp, line unknown]:
  Unknown left-hand 'nslist' in parameter file

checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Cleaning up temporary file gromppYyltp4

-------------------------------------------------------
Program grompp, VERSION 3.3.2
Source code file: toputil.c, line: 61

Fatal error:
Atomtype 'C' not found!
-------------------------------------------------------

"That Was Pretty Cool" (Beavis)

and tfe.pdb is :

REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
MODEL        1
HETATM    1  C1  UNK     1      -0.080   1.504   0.000  1.00  0.00           C
HETATM    2  C2  UNK     1       0.741   0.249   0.000  1.00  0.00           C
HETATM    3  O1  UNK     1       0.380   1.963   0.000  1.00  0.00           O
HETATM    4  F1  UNK     1      -0.096  -0.849   0.000  1.00  0.00           F
HETATM    5  F2  UNK     1       1.537   0.219  -1.127  1.00  0.00           F
HETATM    6  F3  UNK     1       1.537   0.219   1.127  1.00  0.00           F
HETATM    7  H1  UNK     1      -0.031   2.830   0.000  1.00  0.00           H
CONECT    1    2    3
CONECT    2    1    4    5    6
CONECT    3    1    7
CONECT    7    3
CONECT    4    2
CONECT    5    2
CONECT    6    2
ENDMDL

and topology is


;	PEPTIDE A5 OR AUREIN 1.2
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Protein_A           3

[ atoms ]
\\\
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spce.itp"
; Include tfe topology
#include "tfe.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
PEPTIDE A5 OR AUREIN 1.2 in water

[ molecules ]
; Compound        #mols
Protein_A           1
SOL              1308
TFE               40


--again thanks .
sh-karbalaee