[gmx-users] TIP4P water model
Ankita naithani
ankitanaithani at gmail.com
Sun Sep 23 20:28:12 CEST 2012
Hi,
So the commands from the beginning are appended below:
pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro
(I choose option 6 for AMBER99sb-ILDN force field and then option 2
for TIP4P water model)
editconf -f system.gro -o system_box.gro -c -d 1.0 -bt dodecahedron
genbox -cp system_box.gro -cs tip4p.gro -o system_solv.gro -p topol.top
grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
And it is here that I get the error :
Fatal error:
number of coordinates in coordinate file (system_solv.gro, 421880)
does not match topology (topol.top, 416008)
I am appending below the contents of my topology file:
;
; File 'topol.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Fri Sep 21 14:02:35 2012
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx_d - VERSION 4.5.5
;
; Command line was:
; /usr/local/src/gromacs/bin/pdb2gmx_d -vsite h -f 3HQN_tet-nolig.pdb
-o system.gro
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_A2.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_B2.itp"
#include "topol_Protein_chain_C.itp"
#include "topol_Protein_chain_C2.itp"
#include "topol_Protein_chain_D.itp"
#include "topol_Protein_chain_D2.itp"
; Include water topology
#include "amber99sb-ildn.ff/tip4p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_A2 1
Protein_chain_B 1
Protein_chain_B2 1
Protein_chain_C 1
Protein_chain_C2 1
Protein_chain_D 1
Protein_chain_D2 1
SOL 340
SOL 394
SOL 340
SOL 394
SOL 94333
-------------------------------
I cannot understand as to why it is generating error at this stage. It
would be really helpful if you could advice me how to proceed from
here.
Best Wishes,
Ankita
On Sat, Sep 22, 2012 at 12:57 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/21/12 7:55 PM, Peter C. Lai wrote:
>>
>> Perhaps genion is not removing the dummy atoms properly?
>>
>
> The problem is occurring with grompp before genion. We would need to see
> all the prior commands (exactly copied and pasted from the terminal) as well
> as the [molecules] section of the topology, to at least start to guess at
> what's wrong. It is unusual to find a failure in grompp before genion.
>
> -Justin
>
>
>> On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote:
>>>
>>> Hi all,
>>>
>>> I am trying to begin a simulation of a protein.
>>>
>>> I am using AMBER99sb-ILDN force field and TIP4P water model. However,
>>> I am facing a problem in the ion adding step.
>>>
>>> when I issue the grompp command to generate the necessary .tpr file
>>> for simulation to be utilised by genion tool, I get the following
>>> error :
>>>
>>> "Fatal error:
>>> number of coordinates in coordinate file (system_solv.gro, 421880)
>>> does not match topology (topol.top, 416008)
>>> "
>>>
>>> However, I have rechecked several times my topology file and the
>>> co-ordinate file and I am running it pretty straightforward to get
>>> this error. When I try TIP3P water model for the same protein, I do
>>> not get the error.
>>>
>>> I get the same error when I use TIP4P-Ew water model too. I have
>>> decide a better water model for my system before I run my final
>>> production simulations and so I have been trying to compare both the
>>> water models. I am wondering if anyone could kindly suggest the
>>> possible reason for this error because ideally, it should not be
>>> giving me any error at this stage as I haven't manipulated with
>>> anything.
>>>
>>> I am also appending my ions.mdp info below:
>>>
>>> ; ions.mdp - used as input into grompp to generate ions.tpr
>>> ; Parameters describing what to do, when to stop and what to save
>>> integrator = steep ; Algorithm (steep = steepest descent
>>> minimization)
>>> emtol = 1000.0 ; Stop minimization when the maximum
>>> force < 1000.0 kJ/mol/nm
>>> emstep = 0.01 ; Energy step size
>>> nsteps = 50000 ; Maximum number of (minimization) steps
>>> to perform
>>>
>>> ; Parameters describing how to find the neighbors of each atom and how
>>> to calculate the interactions
>>> nstlist = 1 ; Frequency to update the neighbor list
>>> and long range forces
>>> ns_type = grid ; Method to determine neighbor list
>>> (simple, grid)
>>> rlist = 0.9 ; Cut-off for making neighbor list (short
>>> range forces)
>>> coulombtype = PME ; Treatment of long range electrostatic
>>> interactions
>>> rcoulomb = 0.9 ; Short-range electrostatic cut-off
>>> rvdw = 0.9 ; Short-range Van der Waals cut-off
>>> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>>>
>>> -----------
>>>
>>>
>>>
>>> --
>>> Ankita Naithani
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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--
Ankita Naithani
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