[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
anurag.dobhal at nano-medicine.co.in
Tue Sep 30 13:06:19 CEST 2014
Thank you Justin for your reply
as per your suggestion i verified the contents in confout.gro but i was
unable to check file as when i am clicking on it to open it I am getting an
message that file is of unknown type.
I again repeated the tutorial and I am getting the same things.
Thank you again for your time.
On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 9/30/14 5:51 AM, Anurag Dobhal wrote:
>> Hello gromacs users.
>> I am running GROMACS Tutorial of KALP15 in DPPC.
>> I am in the step define box and solvate.
>> after the command
>> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
>> i am getting an error as
>> Use of uninitialized value $box_x in multiplication (*) at
>> inflategro.pl line 339.
>> Use of uninitialized value $box_y in multiplication (*) at
>> inflategro.pl line 340.
>> Scaling lipids....
>> There are 0 lipids...
>> Illegal division by zero at inflategro.pl line 380.
>> I am repeating the step third time and I am getting the same error.
>> please help me how to skip this error.
> I suggested you verify the contents of confout.gro are sensible. What did
> you learn?
> 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
> 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