[gmx-users] tfe

[Justin A. Lemkul]

Comments are embedded throughout.  There are several errors, some related to 
your problem, and others that you should definitely fix before you expect to run 
any real dynamics.

shahrbanoo karbalaee wrote:
> 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
> 

I would fix these, if you haven't already!  Otherwise, you won't get the 
dynamics you expect...

> 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!
> -------------------------------------------------------
> 

Without seeing the contents of tfe.itp, the best I can guess is this: you've 
declared #include "ffoplsaa.itp" (as shown below), but you're using an atomtype 
called "C," which, if you look for such an atomtype within ffoplsaa.atp, you 
will not find.  Thus, unless you have defined additional atomtypes within 
tfe.itp, you will always get this message.

> "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
> 

Are you sure your model is compatible with OPLS-AA?  You don't have all the 
hydrogens on the alcohol carbon...CF3CH2OH, right?

> 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
> 

Don't break up information about water!  The [ position_restraints ] section 
must follow #define "spce.itp," otherwise it will be assigned to TFE.

-Justin

> ; 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
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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