[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

Anurag Dobhal anurag.dobhal at nano-medicine.co.in
Thu Oct 2 14:50:17 CEST 2014

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
> ==================================================
> --
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.



*This communication is intended only for the person or entity to which it 
is addressed and may contain confidential and / or privileged material. Any 
review, retransmission, dissemination or other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
material from your computer. Kindly note that this mail does not constitute 
an offer or solicitation for the purchase or sale of any financial 
instrument or as an official confirmation of any transaction. The 
information is not warranted as to completeness or accuracy and is subject 
to change without notice. Any comments or statements made herein do not 
necessarily reflect those of Nanomedicine Research Group.  Before opening 
the email or accessing any attachments, please check and scan for virus.*

More information about the gromacs.org_gmx-users mailing list