[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Wed Aug 6 12:54:50 CEST 2014
hello everyone
i have been resolved the problem (del 0-23) all the elements
but in output i got lots of warning
WARNING: distance between atoms 9299 and 9301 > 0.3 nm (0.444934).
Index file might be corrupt.
WARNING: distance between atoms 9351 and 9353 > 0.3 nm (1.707690).
Index file might be corrupt.
WARNING: distance between atoms 9403 and 9405 > 0.3 nm (0.766144).
Index file might be corrupt.
WARNING: distance between atoms 9455 and 9457 > 0.3 nm (0.998167).
Index file might be corrupt.
WARNING: distance between atoms 9507 and 9509 > 0.3 nm (1.222285).
Index file might be corrupt.
WARNING: distance between atoms 9559 and 9561 > 0.3 nm (1.553503).
Index file might be corrupt.
WARNING: distance between atoms 9611 and 9613 > 0.3 nm (1.482685).
Index file might be corrupt.
WARNING: distance between atoms 9663 and 9665 > 0.3 nm (2.503910).
Index file might be corrupt.
WARNING: distance between atoms 9715 and 9717 > 0.3 nm (2.239060).
Index file might be corrupt.
WARNING: distance between atoms 9767 and 9769 > 0.3 nm (1.539310).
Index file might be corrupt.
WARNING: distance between atoms 9819 and 9821 > 0.3 nm (1.870721).
Index file might be corrupt.
WARNING: distance between atoms 9871 and 9873 > 0.3 nm (0.994241).
Index file might be corrupt.
WARNING: distance between atoms 9923 and 9925 > 0.3 nm (0.877714).
Index file might be corrupt.
WARNING: distance between atoms 9975 and 9977 > 0.3 nm (1.055654).
Index file might be corrupt.
WARNING: distance between atoms 10027 and 10029 > 0.3 nm (2.673426).
Index file might be corrupt.
WARNING: distance between atoms 10079 and 10081 > 0.3 nm (0.508628).
Index file might be corrupt.
WARNING: distance between atoms 10131 and 10133 > 0.3 nm (1.606320).
Index file might be corrupt.
WARNING: distance between atoms 10183 and 10185 > 0.3 nm (2.219379).
Index file might be corrupt.
WARNING: distance between atoms 10235 and 10237 > 0.3 nm (1.061357).
Index file might be corrupt.
Last frame 500 time 1000.000
Read trajectory. Printing parameters to file
Atom 1 Tensor: x=-0.181426 , y=-0.143345, z=0.324772
Atom 2 Tensor: x=-0.185547 , y=-0.161326, z=0.346873
Atom 3 Tensor: x=-0.181696 , y=-0.16099, z=0.342686
Atom 4 Tensor: x=-0.182835 , y=-0.155051, z=0.337885
Atom 5 Tensor: x=-0.181605 , y=-0.155339, z=0.336944
Atom 6 Tensor: x=-0.17595 , y=-0.14099, z=0.31694
Atom 7 Tensor: x=-0.170447 , y=-0.128763, z=0.29921
Atom 8 Tensor: x=-0.160542 , y=-0.113414, z=0.273956
Atom 9 Tensor: x=-0.148854 , y=-0.107146, z=0.256
Atom 10 Tensor: x=-0.14454 , y=-0.0972709, z=0.241811
Atom 11 Tensor: x=-0.132997 , y=-0.0877024, z=0.2207
Atom 12 Tensor: x=-0.122269 , y=-0.0804395, z=0.202709
Atom 13 Tensor: x=-0.104357 , y=-0.0712167, z=0.175573
Atom 14 Tensor: x=-0.089655 , y=-0.0533254, z=0.14298
Atom 15 Tensor: x=0.101725 , y=0.208169, z=-0.309894
Atom 16 Tensor: x=0.0488879 , y=0.247333, z=-0.296221
i do'nt know what is this
kindly help
On Wed, Aug 6, 2014 at 3:42 PM, RINU KHATTRI <nickname.mittu at gmail.com> wrote:
> hello every one
> i am working on complex with popc membrane i got error in Deuterium
> Order Parameters group 1 does not have same number of elements as grp
> 1
> i used the command
>
> make_ndx -f md_0_1.tpr -o sn1.ndx
> 0 System : 38483 atoms
> 1 Protein : 3873 atoms
> 2 Protein-H : 3061 atoms
> 3 C-alpha : 408 atoms
> 4 Backbone : 1224 atoms
> 5 MainChain : 1633 atoms
> 6 MainChain+Cb : 2015 atoms
> 7 MainChain+H : 2000 atoms
> 8 SideChain : 1873 atoms
> 9 SideChain-H : 1428 atoms
> 10 Prot-Masses : 3873 atoms
> 11 non-Protein : 34610 atoms
> 12 Other : 6365 atoms
> 13 UNK : 21 atoms
> 14 POPC : 6344 atoms
> 15 CL : 15 atoms
> 16 Water : 28230 atoms
> 17 SOL : 28230 atoms
> 18 non-Water : 10253 atoms
> 19 Ion : 15 atoms
> 20 UNK : 21 atoms
> 21 POPC : 6344 atoms
> 22 CL : 15 atoms
> 23 Water_and_ions : 28245 atoms
>
> nr : group ! 'name' nr name 'splitch' nr Enter: list groups
> 'a': atom & 'del' nr 'splitres' nr 'l': list residues
> 't': atom type | 'keep' nr 'splitat' nr 'h': help
> 'r': residue 'res' nr 'chain' char
> "name": group 'case': case sensitive 'q': save and quit
> 'ri': residue index
>
>> aC34
>
> Found 122 atoms with name C34
>
> 24 C34 : 122 atoms
>
>> aC36
>
> Found 122 atoms with name C36
>
> 25 C36 : 122 atoms
>
>> a C37
>
> Found 122 atoms with name C37
>
> 26 C37 : 122 atoms
>
>> a C38
>
> Found 122 atoms with name C38
>
> 27 C38 : 122 atoms
>
>> a C39
>
> Found 122 atoms with name C39
>
> 28 C39 : 122 atoms
>
>> a C40
>
> Found 122 atoms with name C40
>
> 29 C40 : 122 atoms
>
>> a C41
>
> Found 122 atoms with name C41
>
> 30 C41 : 122 atoms
>
>> a C42
>
> Found 122 atoms with name C42
>
> 31 C42 : 122 atoms
>
>> A C43
>
>
> Syntax error: "A C43"
>
>> a C43
>
> Found 122 atoms with name C43
>
> 32 C43 : 122 atoms
>
>> a C44
>
> Found 122 atoms with name C44
>
> 33 C44 : 122 atoms
>
>> a C45
>
> Found 122 atoms with name C45
>
> 34 C45 : 122 atoms
>
>> a C46
>
> Found 122 atoms with name C46
>
> 35 C46 : 122 atoms
>
>> a C47
>
> Found 122 atoms with name C47
>
> 36 C47 : 122 atoms
>
>> a C48
>
> Found 122 atoms with name C48
>
> 37 C48 : 122 atoms
>
>> a C49
>
> Found 122 atoms with name C49
>
> 38 C49 : 122 atoms
>
>> a C50
>
> Found 122 atoms with name C50
>
> 39 C50 : 122 atoms
>
>> a CA1
>
> Found 122 atoms with name CA1
>
> 40 CA1 : 122 atoms
>
>> a CA2
>
> Found 122 atoms with name CA2
>
> 41 CA2 : 122 atoms
>
>> del 0-21
>
> Removed group 0 'System'
> Removed group 1 'Protein'
> Removed group 2 'Protein-H'
> Removed group 3 'C-alpha'
> Removed group 4 'Backbone'
> Removed group 5 'MainChain'
> Removed group 6 'MainChain+Cb'
> Removed group 7 'MainChain+H'
> Removed group 8 'SideChain'
> Removed group 9 'SideChain-H'
> Removed group 10 'Prot-Masses'
> Removed group 11 'non-Protein'
> Removed group 12 'Other'
> Removed group 13 'UNK'
> Removed group 14 'POPC'
> Removed group 15 'CL'
> Removed group 16 'Water'
> Removed group 17 'SOL'
> Removed group 18 'non-Water'
> Removed group 19 'Ion'
> Removed group 20 'UNK'
> Removed group 21 'POPC'
>> q
> 0 System : 38483 atoms
> 1 Protein : 3873 atoms
> 2 Protein-H : 3061 atoms
> 3 C-alpha : 408 atoms
> 4 Backbone : 1224 atoms
> 5 MainChain : 1633 atoms
> 6 MainChain+Cb : 2015 atoms
> 7 MainChain+H : 2000 atoms
> 8 SideChain : 1873 atoms
> 9 SideChain-H : 1428 atoms
> 10 Prot-Masses : 3873 atoms
> 11 non-Protein : 34610 atoms
> 12 Other : 6365 atoms
> 13 UNK : 21 atoms
> 14 POPC : 6344 atoms
> 15 CL : 15 atoms
> 16 Water : 28230 atoms
> 17 SOL : 28230 atoms
> 18 non-Water : 10253 atoms
> 19 Ion : 15 atoms
> 20 UNK : 21 atoms
> 21 POPC : 6344 atoms
> 22 CL : 15 atoms
> 23 Water_and_ions : 28245 atoms
>
> nr : group ! 'name' nr name 'splitch' nr Enter: list groups
> 'a': atom & 'del' nr 'splitres' nr 'l': list residues
> 't': atom type | 'keep' nr 'splitat' nr 'h': help
> 'r': residue 'res' nr 'chain' char
> "name": group 'case': case sensitive 'q': save and quit
> 'ri': residue index
>
>> a C15
>
> Found 122 atoms with name C15
>
> 24 C15 : 122 atoms
>
>> a C17
>
> Found 122 atoms with name C17
>
> 25 C17 : 122 atoms
>
>> a C18
>
> Found 122 atoms with name C18
>
> 26 C18 : 122 atoms
>
>> a C19
>
> Found 122 atoms with name C19
>
> 27 C19 : 122 atoms
>
>> a C20
>
> Found 122 atoms with name C20
>
> 28 C20 : 122 atoms
>
>> a C21
>
> Found 122 atoms with name C21
>
> 29 C21 : 122 atoms
>
>> a C22
>
> Found 122 atoms with name C22
>
> 30 C22 : 122 atoms
>
>> a C23
>
> Found 122 atoms with name C23
>
> 31 C23 : 122 atoms
>
>> a C24
>
> Found 122 atoms with name C24
>
> 32 C24 : 122 atoms
>
>> a C25
>
> Found 122 atoms with name C25
>
> 33 C25 : 122 atoms
>
>> a C26
>
> Found 122 atoms with name C26
>
> 34 C26 : 122 atoms
>
>> a C27
>
> Found 122 atoms with name C27
>
> 35 C27 : 122 atoms
>
>> a C28
>
> Found 122 atoms with name C28
>
> 36 C28 : 122 atoms
>
>> a C29
>
> Found 122 atoms with name C29
>
> 37 C29 : 122 atoms
>
>> a C30
>
> Found 122 atoms with name C30
>
> 38 C30 : 122 atoms
>
>> a C31
>
> Found 122 atoms with name C31
>
> 39 C31 : 122 atoms
>
>> q
>
> mtechbio at mtechbio-HP-Z400-Workstation:~/Desktop/pt1/pt1/epi$ g_order_d
> -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg
>
>
> Taking z axis as normal to the membrane
> Reading file md_0_1.tpr, VERSION 4.5.5 (single precision)
> Using following groups:
> Groupname: CL First atomname: CL First atomnr 38468
> Groupname: Water_and_ions First atomname: OW First atomnr 10238
> Groupname: C34 First atomname: C34 First atomnr 3927
> Groupname: C36 First atomname: C36 First atomnr 3929
> Groupname: C37 First atomname: C37 First atomnr 3930
> Groupname: C38 First atomname: C38 First atomnr 3931
> Groupname: C39 First atomname: C39 First atomnr 3932
> Groupname: C40 First atomname: C40 First atomnr 3933
> Groupname: C41 First atomname: C41 First atomnr 3934
> Groupname: C42 First atomname: C42 First atomnr 3935
> Groupname: C43 First atomname: C43 First atomnr 3936
> Groupname: C44 First atomname: C44 First atomnr 3937
> Groupname: C45 First atomname: C45 First atomnr 3938
> Groupname: C46 First atomname: C46 First atomnr 3939
> Groupname: C47 First atomname: C47 First atomnr 3940
> Groupname: C48 First atomname: C48 First atomnr 3941
> Groupname: C49 First atomname: C49 First atomnr 3942
> Groupname: C50 First atomname: C50 First atomnr 3943
> Groupname: CA1 First atomname: CA1 First atomnr 3944
> Groupname: CA2 First atomname: CA2 First atomnr 3945
>
> Reading frame 0 time 0.000 Number of elements in first group: 15
>
> -------------------------------------------------------
> Program g_order_d, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/tools/gmx_order.c, line: 489
>
> Fatal error:
> grp 1 does not have same number of elements as grp 1
> kindly help
> i didnt get the Dallas Warner post
>
> On Mon, Jul 28, 2014 at 5:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 7/28/14, 1:42 AM, RINU KHATTRI wrote:
>>>
>>> hello everyone
>>>
>>> i used editconf
>>>
>>> editconf -f protein.gro -o protein_newbox.gro -box (membrane box
>>> vectors) -center *x y z*
>>>
>>>
>>> but in z axis i have been increased box size 10.0000 (previously it is
>>> 6.23910 6.17970 6.91950
>>>
>>> http://s48.photobucket.com/user/mittukhattri/media/ri_zpsbb51fbd7.png.html?filters[user]=140927090&filters[recent]=1&sort=1&o=0
>>>
>>> this is the em.gro first minimization image
>>>
>>> mixing of lipid and protein molecule
>>>
>>> kindly help
>>>
>>
>> I don't see any evidence of a problem.
>>
>>
>> -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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