[gmx-users] Fatal error: Atomtype 'CT' not found!

[Yang Ye]

I suspect you still use #include "ffoplsaa.itp" in your topology, i.e.
input.top.

 

Anyway, you may use -pp for grompp to check processed topology and find
whether atom type CT is included.

 

Yang Ye

 

  _____  

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Luciano Costa
Sent: Wednesday, February 15, 2006 1:12 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Fatal error: Atomtype 'CT' not found!

 


Hi gmx' users,

I have tried running gromacs with a diferent force field.  Adjusted by us.

Firstly, I have setted in FF.dat, the new force field, as following:
7
ffG43a1  GROMOS96 43a1 Forcefield (official distribution)
ffG43b1  GROMOS96 43b1 Vacuum Forcefield (official distribution)
ffG43a2  GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
ffoplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
ffoplsaa_new  OPLSAA (modificado por luciano)        <---------- LOOK THIS !
ffgmx    Gromacs Forcefield (see manual)
ffgmx2   gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new
runs)


Then I generated the new files ffoplsaa_new* (.rtp, .atp, -n.tdb, bon.itp
etc.) (9 total).

When I tried run grommp with:

prompt> grompp -v -f grompp.mdp -c input.gro -p input.top  -o -debug

It is shown this message:

#########################################################
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 120 of the 120 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 120 of the 120 1-4 parameter combinations
Cleaning up temporary file gromppTtNKGJ
Fatal error: Atomtype 'CT' not found!
########################################################

The atomtype CT is defined in *.atp, *.rtp, ffoplsaa_newbon.itp and
ffoplsaa_newnb.itp.
I also checked ffoplsaa_new.itp and it is as shown below:
prompt> cat ffoplsaa_new.itp
#define _FF_OPLS
#define _FF_OPLSAA

; This force field uses a format that requires Gromacs 3.1.4 or later.
;
; References for the OPLS-AA force field:
;
; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
; J. Am. Chem. Soc. 118, 11225-11236 (1996).
; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059
(1998).
; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).
; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).
; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001).
; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. Phys.
Chem. B 105, 6474 (2001).
;

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               3               yes             0.5     0.5

;#include "ffoplsaanb.itp"
;#include "ffoplsaabon.itp"
#include "ffoplsaa_newnb.itp"
#include "ffoplsaa_newbon.itp"

What should I do in this case ?! Why the error message ?! 

Best regards,

Luciano.

-- 
### Luciano Tavares da Costa ###
##       
##       100 % Linux
############################# 

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