[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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