[gmx-users] Error in system_inflate.gro coordinates does not match
RINU KHATTRI
nickname.mittu at gmail.com
Wed Aug 6 12:12:25 CEST 2014
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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