[gmx-users] Error in system_inflate.gro coordinates does not match

[RINU KHATTRI]

hello gromacs users
ohk justin but if unk is deleted then how to put it back in
system_inflate.gro


On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
>
>> hello every one
>> I am working on complex with popc membrane i did
>>
>> perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
>>
>> after this step minimization
>>
>> grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
>>
>> i got error
>> Fatal error:
>> number of coordinates in coordinate file (system_inflated.gro, 10224)
>>               does not match topology (topol.top, 10245)
>> i have been removed 6 lipid molecules in my topology file according to
>> output i got one thing new in my system_inflate.gro file the written
>> displayed atom is 10224 but after counting it is 10536 so if i correct it
>> difference is more
>>
>
> I don't know what this means, but the number of atoms that grompp is
> finding is going to be correct.
>
>
>  in topology file [molecule]
>> protein chain 1
>> UNK            1
>> POPC 122
>> how to resolve  it
>>
>
> I would venture a guess that UNK has 21 atoms.  I don't know that
> InflateGRO handles arbitrary molecules, so it may have gotten deleted upon
> inflation. Check system_inflated.gro; it will be very obvious if it is
> missing.
>
> -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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