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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