On 11/13/13 5:51 AM, Atila Petrosian wrote:
Dear Justin

Very thanks for your reply.

I created a new topol.top file as below:

1) I used once default directive.

2) I put cnt.itp file in working directory.

3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp"
in the end of topol.top file. I modified [ molecules ] directive.
begining of topol.top file is as follows:

; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
Protein_chain_A     3

[ atoms ]

end of com.top file is as follows:

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"

#include "cnt.itp"

; Include water topology
#include "charmm27.ff/tip3p.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000

; Include topology for ions
#include "charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
CNT                 1
SOL              1388
Previous error (Invalid order for directive defaults) was solved, but
When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr,
I encountered with this error:

ERROR    1 [file cnt.itp, line 2861]:
   No default Angle types

ERROR 1218 [file cnt.itp, line 4078]:
   No default Angle types

Fatal error:
There were 1218 errors in input file(s).

Lines 2861-4078 are related to [ angles ] directive in cnt.itp file.
How to solve this issue?

In your previous setup, you were effectively trying to use CHARMM27 + some other force field related to the CNT. You can't do that. What you can do (and need to do) is incorporate the nonbonded and bonded parameters related to the CNT into the parent force field. You may be able to simply #include the ffnonbonded.itp and ffbonded.itp files in the topology. Your current approach has simply deleted necessary information.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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