[gmx-users] grompp or parameter file problem?

[Yang Ye]

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 <anna.reymer at gmail.com>
To: gmx-users at 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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