[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

[Anurag Dobhal]

Thanks Justin

I m running the command

 " mdrun -s em.tpr  " and I did get the confout.gro file as output.

after that I am running the command

" perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat "
and then again the energy minimization command.

" mdrun -s em.tpr  "

After that  I am solvating the system.
I did put a local copy of vdwradii.dat in my working directorie  and change
the value of C from 0.15 to 0.375.


 I am solvating my system by the command

" genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p
topol.top "

after that I am adding the ions in the system by the command

" grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr "

But now I am getting an error

number of coordinates in coordinate file (system_solv.gro, 8218)
    does not match topology (topol.top, 1956)


can you please help what caused this error.

Thanking you

On Tue, Sep 30, 2014 at 8:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/30/14 10:30 AM, Anurag Dobhal wrote:
>
>> Dear justin
>>
>> Thank you for your rely and precious time.
>>
>> I am aware that .gro file is to be visualized in VMD and its content can
>> be
>> checked in text editor.
>> all the previous .gro file are visualized and checked in VMD.
>>
>> I have obetained that ( confout.gro )file by running the command of energy
>> minimization i.e.
>>
>> "mdrun -v -deffnm em"
>>
>> and before this command I ran the command
>>
>> "perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat"
>>
>>
>> after running the energy minimization the confout.gro is actually
>> obetained as
>>
>> confout.gro.trr. so I am renaming it as confout.gro. so it is actually
>> .trr format, which can not be visualised in VMD or checked in text
>> editor.
>>
>>
> Which means it's an invalid input file format and that's why you're
> getting a failure from InflateGRO.  If file names are given different
> extensions, you can't just randomly change them and expect things to work.
> If you ran
>
> mdrun -v -deffnm em
>
> you will never get anything named confout.gro.  Note that the tutorial
> explicitly says:
>
> Then, scale down the lipids by a factor of 0.95 (assuming you have used
> default names, the result of the minimization is called "confout.gro"
>
> You didn't use default names.  You told mdrun "name all of my files em.*"
> when you invoked -deffnm.  If you simply ran:
>
> mdrun -s em.tpr
>
> you would get confout.gro.  In any case, you should have "em.gro" which is
> what you should use to proceed.  I have no idea where confout.gro.trr came
> from, but it's a trajectory and clearly not what needs to be used here.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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