[gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

[bhavaniprasad vipperla]

Hi
I tried to run the minimization step . Minimization went on well but am not confout.gro

Is there any specific command for obtaining an confout.gro while running em.
Regards

-----Original Message-----

From: Justin Lemkul
Sent: 3 Aug 2012 14:55:25 GMT
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: number of coordinates in coordinate file   (system_inflated.gro,   9331) number of coordinates in coordinate file does not match topology



On 8/3/12 10:52 AM, bhavaniprasad vipperla wrote:
> Hi Justin
> Could u suggest me which step to carry on further.
>

It's not clear to me that InflateGRO truly failed, though some of the output is
curious, as noted before.

> In place of inflategro , can we use g_membed.
>

Sure. I don't use it personally, but others do.

-Justin

> Regards
> Bhavaniprasad
>
> -----Original Message-----
>
> From: Justin Lemkul
> Sent: 3 Aug 2012 10:54:49 GMT
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Re: number of coordinates in coordinate file   (system_inflated.gro,   9331) number of coordinates in coordinate file does not match topology
>
>
>
> On 8/3/12 12:32 AM, Bhavaniprasad.V wrote:
>> hi justin,
>>
>> the problem is actually InflateGro is not deleting any lipids.
>> I had inserted the protein in lipid using VMD and saved the coordinate file and
>> using that directly to this step
>>
>> cat pro_in_pope.gro pope_whole.gro > system.gro
>>
>> after running perl inflategro.pl system.gro 4 POPE 14 system_inflated.gro 5
>> area.dat.
>> Argument "P8" isn't numeric in printf at inflategro.pl line 708.
>> Argument "O9" isn't numeric in printf at inflategro.pl line 708.
>>
>> Calculating Area per lipid...
>> Protein X-min/max: -4    103
>> Protein Y-min/max: -14    100
>> X-range: 107 A    Y-range: 114 A
>> Building 107 X 114 2D grid on protein coordinates...
>> Calculating area occupied by protein..
>> full TMD..
>> upper TMD....
>> lower TMD....
>> Area per protein: 107.75 nm^2
>> Area per lipid: 8.02906194817911 nm^2
>>
>> Area per protein, upper half: 101.25 nm^2
>> Area per lipid, upper leaflet : 8.09202321149701 nm^2
>>
>> Area per protein, lower half: 102.25 nm^2
>> Area per lipid, lower leaflet : 8.03790402571429 nm^2
>>
>> Writing Area per lipid...
>> Done!
>>
>> So please suggest me what is going wrong
>>
>
> The errors above indicate something is going wrong with printing the output, but
> from looking at the code I see no reason why this should come up.  It is also
> quite possible that no lipids need to be deleted based on the inflated structure.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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