Hi Yang!
DNA is called protein.
ffamber_tip3p.itp is ancluded in the topology file.
Initially, when I run pdb2gmx I use an option -water and specify it to 'tip3p'
Here are some excerpt from my top file:
beginning:
------------------
; Include forcefield parameters
#include "ffamber99.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 amber99_25 1 DC5 H5T 1 0.4422 1.008
; qtot 0.4422
2 amber99_43 1 DC5 O5' 2 -0.6318 16
; qtot -0.1896
3 amber99_11 1 DC5 C5' 3 -0.0069 12.01
; qtot -0.1965
4 amber99_19 1 DC5 H5'1 4 0.0754 1.008
; qtot -0.1211
5 amber99_19 1 DC5 H5'2 5 0.0754 1.008
; qtot -0.0457
....................................
end
-------
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "tip3p.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
DICKERSON DODECAMER in water
[ molecules ]
; Compound #mols
Protein 1
SOL 10682
--------------
Thank you very much for your help!!!
regards
/anna
On 6/20/07, Yang Ye <[EMAIL PROTECTED]> wrote:
What's the name for DNA under [ moleculetype ] in your top file?
Another question is: have you included ffamber_tip3p.itp?
Probably you need to post excerpt of your topology here if you are not sure
about your answers towards above two questions.
Regards,
Yang Ye
----- Original Message ----
From: Anna Reymer <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Wednesday, June 20, 2007 10:57:28 PM
Subject: [gmx-users] grompp or parameter file problem?
Hello all!
I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port.
I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro.
When running grompp:
grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr
with the following em.mdp:
-------------------------------------
; DNA energy minimization in water
;
cpp = /lib/cpp -traditional
define =
include = -I/***/share/gromacs/top/ffamber99.itp
constraints = none
integrator = cg
nsteps = 1000
;
; ENERGY MINIZATION STUFF
;
emtol = 2000
emstep = 0.01
nstcgsteep = 100
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
I get the fatal error message:
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448
Fatal error:
number of coordinates in coordinate file (genbox.gro, 32804)
does not match topology (dick.top, 0)
-------------------------------------------------------
Top file has all includes and its tail looks:
[ molecules ]
; Compound #mols
Protein 1
SOL 10682
---------------------------------------------------------
Does somebody have similar problems? Has somebody solved them?
I will appreciate any help!
regards
/anna
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