[gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
jalemkul at vt.edu
Fri Aug 3 16:54:40 CEST 2012
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.
> -----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
>> 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...
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> * Only plain text messages are allowed!
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users