[gmx-users] confout.gro

[RINU KHATTRI]

hello gromacs users
i am applying (solv.gro 101917-108573 topol.top )/3
=     i have to subtract 2218.66 into old figure (32672 which is present in
topol.top )
due to float no still error persist only one coordinate is different
Fatal error:
number of coordinates in coordinate file (solv.gro, 101917)
             does not match topology (topol.top, 101916)
how to resolve
i have been apply all the numbers in float but still difference
help


On Mon, Jul 7, 2014 at 2:06 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello everyone
> after this step now i am in the
>  grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
> step but after running i got error
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 101917)  does not
> match topology (topol.top, 604599)
> i have been edited the sol (counted from solv.gro) but still error how to
> resolve it infact figure is increased
>
>
>
> On Mon, Jul 7, 2014 at 12:05 PM, RINU KHATTRI <nickname.mittu at gmail.com>
> wrote:
>
>> hello gromacs users
>> thanks justin i have applied
>>
>> perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat
>>
>> mdrun -v -deffnm em
>>
>> perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
>> area_shrink1.dat
>>
>> after that solvation step but no command is present in dppc tutorial
>> should i used
>>
>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>
>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>
>> but conf.gro is the combined file of (b3_procesed.gro+ drg.itp)
>>
>> is it this file or em.gro which is formed 2 step before this
>>
>>
>>
>>
>>
>>
>>
>> On Sat, Jul 5, 2014 at 4:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 7/5/14, 12:51 AM, RINU KHATTRI wrote:
>>>
>>>> hello gromacs users
>>>> but i am confussed if confout.gro is input, in which step it is formed
>>>> according to tutorial before this step the step is
>>>> perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat
>>>> is system_inflated.gro is confout.gro or which gro file i must be used
>>>> as confout.gro
>>>>
>>>> perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5
>>>> area_shrink1.dat
>>>>
>>>
>>> The file "confout.gro" is the default name of the final output
>>> coordinates of an mdrun process, unless you provide a different file name
>>> to mdrun -c.  In this case, the protocol is:
>>>
>>> 1. Inflate the system (produce system_inflated.gro)
>>> 2. Minimize the inflated system (produce confout.gro, unless otherwise
>>> named)
>>> 3. Begin shrinking the system, starting with the output of step 2.
>>>
>>> So "confout.gro" is the _output_ of step 2 and the _input_ of step 3.
>>>
>>> -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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>>
>>
>