[gmx-users] include file mechanism pope.itp in protein-membrane system

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 9 15:43:12 CET 2009



irene farabella wrote:
> Hi!!
> 
> I am using the include file mechanism to define the topology of my 
> protein-membrane system.
> I have a problem regarding the pope.itp file. I use a modified version 
> of the pope.itp from 
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies 
> (see below).That is accordingly with the pdb file that I am using ( see 
> bellow). However when using grompp I got this warning:
> 
> Warning: atom name 7542 in papc_topol2.top and system-clean-120xy.pdb 
> does not match (H1 - N)
> Warning: atom name 7543 in papc_topol2.top and system-clean-120xy.pdb 
> does not match (O1 - H1)
> Warning: atom name 7544 in papc_topol2.top and system-clean-120xy.pdb 
> does not match (CA - H2)
> 
> as if none of the atoms that belong to pope in the pdb match the 
> respective itp file.
> Maybe I am wrong but seems to me that the the atoms are actually matching..
> any suggestions are welcome...

Well, if you've modified the pope.itp file, then that could be a source of 
error, but without substantially more information about what you've done, 
there's nothing to comment on there.

The other potential problem is that the content of the [molecules] directive 
must be the same as the order of the species in the coordinate file.  You may be 
seeing mismatches because things are out of place in the topology.

-Justin

> 
> Irene
> 
> ----system.top---
> #include "ffoplsaa.itp"
> #include "protein-only.itp"
> #include "pope.itp"
> #include "popg.itp"
> #include "tip3p.itp"
> #include "ions.itp"
> ....
> ---pope.itp---
> [ atoms ]
> ;   nr    type   resnr  residu    atom    cgnr        charge          mass
>     1     LNL       1    POPE      N      0        -0.5000   14.0067    
> ; qtot:0.7
>     2      H        1    POPE     H1      0         0.4000   1.0080    ; 
> qtot:0.36  
>     3      H        1    POPE     H2      0         0.4000   1.0080    ; 
> qtot:0.72
>     4      H        1    POPE     H3      0         0.4000   1.0008    ; 
> qtot:1.08
>     5     LH2       1    POPE     CA      0         0.3000   14.0270    
> ; qtot:1.0
>     6     LC2       1    POPE     CB      1         0.4000   14.0270    
> ; qtot:1.0
>     7     LP        1    POPE      P      1         1.700    30.9738    
> ; qtot:2.3 
>     8     LOM       1    POPE     OB      1        -0.800    15.9994    
> ; qtot:1.5
>     9     LOM       1    POPE     OC      1        -0.800    15.9994    
> ; qtot:0.7
>    10     LOS       1    POPE     OD      1        -0.700    15.9994    
> ; qtot:0    
>    11     LOS       1    POPE     OA      1        -0.800    15.9994    
> ; qtot:0.54
>    12     LC2       1    POPE     CC      2         0.400    14.0270    
> ; qtot:0.08
>    13     LH1       1    POPE     CD      2         0.300    13.0190    
> ; qtot:0.52
>    14     LOS       1    POPE     OG      2        -0.700    15.9994    
> ; qtot:-0.14
>    15      LC       1    POPE    C2A      2         0.7000   12.0110    
> ; qtot:0.56
>    16      LO       1    POPE     OH      2        -0.700    15.9994    
> ; qtot:0.0
>    17     LP2       1    POPE    C2B      3         0.0      14.0270    
> ; qtot:
>    18     LC2       1    POPE     CE      4          0.50    14.0270    
> ; qtot:
>    19     LOS       1    POPE     OE      4         -0.70    15.9994    
> ; qtot:  
>    20      LC       1    POPE    C1A      4          0.80    12.0110    
> ; qtot:
>    21      LO       1    POPE     OF      4         -0.60    15.9994    
> ; qtot:
>    22     LP2       1    POPE    C1B      5           0    14.0270    ; 
> qtot:
>    23     LP2       1    POPE    C2C      6           0    14.0270    ; 
> qtot:
>    24     LP2       1    POPE    C2D      7           0    14.0270    ; 
> qtot:
>    25     LP2       1    POPE    C2E      8           0    14.0270    ; 
> qtot:
>    26     LP2       1    POPE    C2F      9           0    14.0270    ; 
> qtot:
>    27     LP2       1    POPE    C2G      10          0    14.0270    ; 
> qtot:
>    28     LP2       1    POPE    C2H      11          0    14.0270    ; 
> qtot:
>    29     LH1       1    POPE    C2I      12          0    13.0190    ; 
> qtot:
>    30     LH1       1    POPE    C2J      13          0    13.0190    ; 
> qtot:
>    31     LP2       1    POPE    C2K      14          0    14.0270    ; 
> qtot:
>    32     LP2       1    POPE    C2L      15          0    14.0270    ; 
> qtot:
>    33     LP2       1    POPE    C2M      16          0    14.0270    ; 
> qtot:
>    34     LP2       1    POPE    C2N      17          0    14.0270    ; 
> qtot:
>    35     LP2       1    POPE    C2O      18          0    14.0270    ; 
> qtot:
>    36     LP2       1    POPE    C2P      19          0    14.0270    ; 
> qtot:
>    37     LP2       1    POPE    C2Q      20          0    14.0270   ; tail2
>    38     LP3       1    POPE    C2R      21          0    15.0350   ; tail2
>    39     LP2       1    POPE    C1C      22          0    14.0270    ; 
> qtot:
>    40     LP2       1    POPE    C1D      23          0    14.0270    ; 
> qtot:
>    41     LP2       1    POPE    C1E      24          0    14.0270    ; 
> qtot:
>    42     LP2       1    POPE    C1F      25          0    14.0270    ; 
> qtot:
>    43     LP2       1    POPE    C1G      26          0    14.0270    ; 
> qtot:
>    44     LP2       1    POPE    C1H      27          0    14.0270    ; 
> qtot:
>    45     LP2       1    POPE    C1I      28          0    14.0270    ; 
> qtot:
>    46     LP2       1    POPE    C1J      29          0    14.0270    ; 
> qtot:
>    47     LP2       1    POPE    C1K      30          0    14.0270    ; 
> qtot:
>    48     LP2       1    POPE    C1L      31          0    14.0270    ; 
> qtot:
>    49     LP2       1    POPE    C1M      32          0    14.0270    ; 
> qtot:
>    50     LP2       1    POPE    C1N      33          0    14.0270    ; 
> qtot:
>    51     LP2       1    POPE    C1O      34          0    14.0270    ; 
> qtot:
>    52     LP3       1    POPE    C1P      35          0    15.0350    ; 
> qtot:
> ......
> ----part of system.pdb---
> ATOM   7538  HA2 GLY   492     -15.928  25.565  -9.225  1.00  0.00      PROA
> ATOM   7539  C   GLY   492     -17.547  24.935  -8.009  1.00  0.00      PROA
> ATOM   7540  O1  GLY   492     -17.919  23.755  -7.770  1.00  0.00      PROA
> ATOM   7541  O2  GLY   492     -17.643  25.885  -7.186  1.00  0.00      PROA
> ATOM   7542  N   POPE    1      36.404 -26.235  18.738  1.00  0.00      MEMB
> ATOM   7543  H1  POPE    1      35.597 -25.926  18.160  1.00  0.00      MEMB
> ATOM   7544  H2  POPE    1      36.945 -25.351  18.819  1.00  0.00      MEMB
> ATOM   7545  H3  POPE    1      36.936 -26.902  18.142  1.00  0.00      MEMB
> ATOM   7546  CA  POPE    1      36.015 -26.805  20.058  1.00  0.00      MEMB
> ATOM   7549  CB  POPE    1      34.808 -27.824  19.956  1.00  0.00      MEMB
> ATOM   7552  P   POPE    1      34.292 -30.182  19.000  1.00  0.00      MEMB
> ATOM   7553  OB  POPE    1      33.512 -30.641  20.257  1.00  0.00      MEMB
> ATOM   7554  OC  POPE    1      34.949 -31.147  18.138  1.00  0.00      MEMB
> ATOM   7555  OD  POPE    1      33.197 -29.423  18.147  1.00  0.00      MEMB
> ATOM   7556  OA  POPE    1      35.265 -29.013  19.393  1.00  0.00      MEMB
> ATOM   7557  CC  POPE    1      33.571 -28.743  16.936  1.00  0.00      MEMB
> ATOM   7560  CD  POPE    1      32.690 -29.147  15.737  1.00  0.00      MEMB
> ATOM   7562  OG  POPE    1      33.077 -28.322  14.669  1.00  0.00      MEMB
> ATOM   7563  C2A POPE    1      33.797 -28.763  13.631  1.00  0.00      MEMB
> ATOM   7564  OH  POPE    1      34.161 -29.917  13.395  1.00  0.00      MEMB
> ATOM   7565  C2B POPE    1      34.062 -27.508  12.738  1.00  0.00      MEMB
> ATOM   7568  CE  POPE    1      31.183 -28.987  16.177  1.00  0.00      MEMB
> ATOM   7571  OE  POPE    1      30.226 -29.124  15.041  1.00  0.00      MEMB
> ATOM   7572  C1A POPE    1      28.957 -29.323  15.472  1.00  0.00      MEMB
> ATOM   7573  OF  POPE    1      28.586 -29.516  16.626  1.00  0.00      MEMB
> ATOM   7574  C1B POPE    1      28.010 -29.304  14.251  1.00  0.00      MEMB
> ATOM   7577  C2C POPE    1      34.969 -27.819  11.519  1.00  0.00      MEMB
> ATOM   7580  C2D POPE    1      36.351 -28.241  11.876  1.00  0.00      MEMB
> ATOM   7583  C2E POPE    1      37.380 -28.558  10.740  1.00  0.00      MEMB
> ATOM   7586  C2F POPE    1      37.180 -29.921   9.973  1.00  0.00      MEMB
> ATOM   7589  C2G POPE    1      38.104 -30.071   8.659  1.00  0.00      MEMB
> ATOM   7592  C2H POPE    1      39.581 -29.831   8.812  1.00  0.00      MEMB
> ATOM   7595  C2I POPE    1      40.122 -30.691   9.962  1.00  0.00      MEMB
> ATOM   7597  C2J POPE    1      40.655 -31.917   9.901  1.00  0.00      MEMB
> ATOM   7599  C2K POPE    1      41.092 -32.715   8.743  1.00  0.00      MEMB
> ATOM   7602  C2L POPE    1      40.818 -34.234   8.782  1.00  0.00      MEMB
> ATOM   7605  C2M POPE    1      41.327 -34.842   7.433  1.00  0.00      MEMB
> ATOM   7608  C2N POPE    1      40.591 -36.070   6.960  1.00  0.00      MEMB
> ATOM   7611  C2O POPE    1      39.217 -35.763   6.310  1.00  0.00      MEMB
> ATOM   7614  C2P POPE    1      38.505 -36.897   5.729  1.00  0.00      MEMB
> ATOM   7617  C2Q POPE    1      38.072 -37.966   6.771  1.00  0.00      MEMB
> ATOM   7620  C2R POPE    1      37.186 -39.099   6.129  1.00  0.00      MEMB
> ATOM   7624  C1C POPE    1      28.000 -30.590  13.390  1.00  0.00      MEMB
> ATOM   7627  C1D POPE    1      27.531 -31.928  14.015  1.00  0.00      MEMB
> ATOM   7630  C1E POPE    1      26.853 -32.876  13.038  1.00  0.00      MEMB
> ATOM   7633  C1F POPE    1      26.078 -34.112  13.621  1.00  0.00      MEMB
> ATOM   7636  C1G POPE    1      25.077 -34.649  12.517  1.00  0.00      MEMB
> ATOM   7639  C1H POPE    1      23.642 -34.130  12.513  1.00  0.00      MEMB
> ATOM   7642  C1I POPE    1      22.666 -35.170  11.902  1.00  0.00      MEMB
> ATOM   7645  C1J POPE    1      22.744 -35.347  10.415  1.00  0.00      MEMB
> ATOM   7648  C1K POPE    1      21.584 -36.187   9.891  1.00  0.00      MEMB
> ATOM   7651  C1L POPE    1      21.250 -35.906   8.447  1.00  0.00      MEMB
> ATOM   7654  C1M POPE    1      20.075 -36.745   7.992  1.00  0.00      MEMB
> ATOM   7657  C1N POPE    1      19.925 -36.586   6.511  1.00  0.00      MEMB
> ATOM   7660  C1O POPE    1      18.908 -37.540   5.943  1.00  0.00      MEMB
> ATOM   7663  C1P POPE    1      18.457 -37.136   4.599  1.00  0.00      MEMB
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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