<div class="gmail_quote">Hi!!<br><br>I am using the include file mechanism to define the topology of my protein-membrane system.<br>I have a problem regarding the pope.itp file. I use a modified version of the pope.itp from <a href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies" target="_blank">http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies</a> (see below).That is accordingly with the pdb file that I am using ( see bellow). However when using grompp I got this warning:<br>
<br>Warning: atom name 7542 in papc_topol2.top and system-clean-120xy.pdb does not match (H1 - N)<br>Warning: atom name 7543 in papc_topol2.top and system-clean-120xy.pdb does not match (O1 - H1)<br>Warning: atom name 7544 in papc_topol2.top and system-clean-120xy.pdb does not match (CA - H2)<br>
<br>as if none of the atoms that belong to pope in the pdb match the respective itp file.<br>Maybe I am wrong but seems to me that the the atoms are actually matching..<br>any suggestions are welcome...<br><br>Irene<br><br>
----system.top---<br>
#include "ffoplsaa.itp"<br>#include "protein-only.itp"<br>#include "pope.itp"<br>#include "popg.itp"<br>#include "tip3p.itp"<br>#include "ions.itp"<br>....<br>---pope.itp---<br>
[ atoms ]<br>; nr type resnr residu atom cgnr charge mass<br> 1 LNL 1 POPE N 0 -0.5000 14.0067 ; qtot:0.7<br> 2 H 1 POPE H1 0 0.4000 1.0080 ; qtot:0.36 <br>
3 H 1 POPE H2 0 0.4000 1.0080 ; qtot:0.72 <br> 4 H 1 POPE H3 0 0.4000 1.0008 ; qtot:1.08 <br> 5 LH2 1 POPE CA 0 0.3000 14.0270 ; qtot:1.0 <br>
6 LC2 1 POPE CB 1 0.4000 14.0270 ; qtot:1.0 <br> 7 LP 1 POPE P 1 1.700 30.9738 ; qtot:2.3 <br> 8 LOM 1 POPE OB 1 -0.800 15.9994 ; qtot:1.5<br>
9 LOM 1 POPE OC 1 -0.800 15.9994 ; qtot:0.7<br> 10 LOS 1 POPE OD 1 -0.700 15.9994 ; qtot:0 <br> 11 LOS 1 POPE OA 1 -0.800 15.9994 ; qtot:0.54 <br>
12 LC2 1 POPE CC 2 0.400 14.0270 ; qtot:0.08 <br> 13 LH1 1 POPE CD 2 0.300 13.0190 ; qtot:0.52 <br> 14 LOS 1 POPE OG 2 -0.700 15.9994 ; qtot:-0.14 <br>
15 LC 1 POPE C2A 2 0.7000 12.0110 ; qtot:0.56 <br> 16 LO 1 POPE OH 2 -0.700 15.9994 ; qtot:0.0 <br> 17 LP2 1 POPE C2B 3 0.0 14.0270 ; qtot: <br>
18 LC2 1 POPE CE 4 0.50 14.0270 ; qtot: <br> 19 LOS 1 POPE OE 4 -0.70 15.9994 ; qtot: <br> 20 LC 1 POPE C1A 4 0.80 12.0110 ; qtot: <br>
21 LO 1 POPE OF 4 -0.60 15.9994 ; qtot: <br> 22 LP2 1 POPE C1B 5 0 14.0270 ; qtot: <br> 23 LP2 1 POPE C2C 6 0 14.0270 ; qtot: <br>
24 LP2 1 POPE C2D 7 0 14.0270 ; qtot: <br> 25 LP2 1 POPE C2E 8 0 14.0270 ; qtot: <br> 26 LP2 1 POPE C2F 9 0 14.0270 ; qtot: <br>
27 LP2 1 POPE C2G 10 0 14.0270 ; qtot: <br> 28 LP2 1 POPE C2H 11 0 14.0270 ; qtot: <br> 29 LH1 1 POPE C2I 12 0 13.0190 ; qtot: <br>
30 LH1 1 POPE C2J 13 0 13.0190 ; qtot: <br> 31 LP2 1 POPE C2K 14 0 14.0270 ; qtot: <br> 32 LP2 1 POPE C2L 15 0 14.0270 ; qtot: <br>
33 LP2 1 POPE C2M 16 0 14.0270 ; qtot: <br> 34 LP2 1 POPE C2N 17 0 14.0270 ; qtot: <br> 35 LP2 1 POPE C2O 18 0 14.0270 ; qtot: <br>
36 LP2 1 POPE C2P 19 0 14.0270 ; qtot: <br> 37 LP2 1 POPE C2Q 20 0 14.0270 ; tail2<br> 38 LP3 1 POPE C2R 21 0 15.0350 ; tail2<br>
39 LP2 1 POPE C1C 22 0 14.0270 ; qtot: <br> 40 LP2 1 POPE C1D 23 0 14.0270 ; qtot: <br> 41 LP2 1 POPE C1E 24 0 14.0270 ; qtot: <br>
42 LP2 1 POPE C1F 25 0 14.0270 ; qtot: <br> 43 LP2 1 POPE C1G 26 0 14.0270 ; qtot: <br> 44 LP2 1 POPE C1H 27 0 14.0270 ; qtot: <br>
45 LP2 1 POPE C1I 28 0 14.0270 ; qtot: <br> 46 LP2 1 POPE C1J 29 0 14.0270 ; qtot: <br> 47 LP2 1 POPE C1K 30 0 14.0270 ; qtot: <br>
48 LP2 1 POPE C1L 31 0 14.0270 ; qtot: <br> 49 LP2 1 POPE C1M 32 0 14.0270 ; qtot: <br> 50 LP2 1 POPE C1N 33 0 14.0270 ; qtot: <br>
51 LP2 1 POPE C1O 34 0 14.0270 ; qtot: <br> 52 LP3 1 POPE C1P 35 0 15.0350 ; qtot: <br>......<br>----part of system.pdb---<br>ATOM 7538 HA2 GLY 492 -15.928 25.565 -9.225 1.00 0.00 PROA<br>
ATOM 7539 C GLY 492 -17.547 24.935 -8.009 1.00 0.00 PROA<br>ATOM 7540 O1 GLY 492 -17.919 23.755 -7.770 1.00 0.00 PROA<br>ATOM 7541 O2 GLY 492 -17.643 25.885 -7.186 1.00 0.00 PROA<br>
ATOM 7542 N POPE 1 36.404 -26.235 18.738 1.00 0.00 MEMB<br>ATOM 7543 H1 POPE 1 35.597 -25.926 18.160 1.00 0.00 MEMB<br>ATOM 7544 H2 POPE 1 36.945 -25.351 18.819 1.00 0.00 MEMB<br>
ATOM 7545 H3 POPE 1 36.936 -26.902 18.142 1.00 0.00 MEMB<br>ATOM 7546 CA POPE 1 36.015 -26.805 20.058 1.00 0.00 MEMB<br>ATOM 7549 CB POPE 1 34.808 -27.824 19.956 1.00 0.00 MEMB<br>
ATOM 7552 P POPE 1 34.292 -30.182 19.000 1.00 0.00 MEMB<br>ATOM 7553 OB POPE 1 33.512 -30.641 20.257 1.00 0.00 MEMB<br>ATOM 7554 OC POPE 1 34.949 -31.147 18.138 1.00 0.00 MEMB<br>
ATOM 7555 OD POPE 1 33.197 -29.423 18.147 1.00 0.00 MEMB<br>ATOM 7556 OA POPE 1 35.265 -29.013 19.393 1.00 0.00 MEMB<br>ATOM 7557 CC POPE 1 33.571 -28.743 16.936 1.00 0.00 MEMB<br>
ATOM 7560 CD POPE 1 32.690 -29.147 15.737 1.00 0.00 MEMB<br>ATOM 7562 OG POPE 1 33.077 -28.322 14.669 1.00 0.00 MEMB<br>ATOM 7563 C2A POPE 1 33.797 -28.763 13.631 1.00 0.00 MEMB<br>
ATOM 7564 OH POPE 1 34.161 -29.917 13.395 1.00 0.00 MEMB<br>ATOM 7565 C2B POPE 1 34.062 -27.508 12.738 1.00 0.00 MEMB<br>ATOM 7568 CE POPE 1 31.183 -28.987 16.177 1.00 0.00 MEMB<br>
ATOM 7571 OE POPE 1 30.226 -29.124 15.041 1.00 0.00 MEMB<br>ATOM 7572 C1A POPE 1 28.957 -29.323 15.472 1.00 0.00 MEMB<br>ATOM 7573 OF POPE 1 28.586 -29.516 16.626 1.00 0.00 MEMB<br>
ATOM 7574 C1B POPE 1 28.010 -29.304 14.251 1.00 0.00 MEMB<br>ATOM 7577 C2C POPE 1 34.969 -27.819 11.519 1.00 0.00 MEMB<br>ATOM 7580 C2D POPE 1 36.351 -28.241 11.876 1.00 0.00 MEMB<br>
ATOM 7583 C2E POPE 1 37.380 -28.558 10.740 1.00 0.00 MEMB<br>ATOM 7586 C2F POPE 1 37.180 -29.921 9.973 1.00 0.00 MEMB<br>ATOM 7589 C2G POPE 1 38.104 -30.071 8.659 1.00 0.00 MEMB<br>
ATOM 7592 C2H POPE 1 39.581 -29.831 8.812 1.00 0.00 MEMB<br>ATOM 7595 C2I POPE 1 40.122 -30.691 9.962 1.00 0.00 MEMB<br>ATOM 7597 C2J POPE 1 40.655 -31.917 9.901 1.00 0.00 MEMB<br>
ATOM 7599 C2K POPE 1 41.092 -32.715 8.743 1.00 0.00 MEMB<br>ATOM 7602 C2L POPE 1 40.818 -34.234 8.782 1.00 0.00 MEMB<br>ATOM 7605 C2M POPE 1 41.327 -34.842 7.433 1.00 0.00 MEMB<br>
ATOM 7608 C2N POPE 1 40.591 -36.070 6.960 1.00 0.00 MEMB<br>ATOM 7611 C2O POPE 1 39.217 -35.763 6.310 1.00 0.00 MEMB<br>ATOM 7614 C2P POPE 1 38.505 -36.897 5.729 1.00 0.00 MEMB<br>
ATOM 7617 C2Q POPE 1 38.072 -37.966 6.771 1.00 0.00 MEMB<br>ATOM 7620 C2R POPE 1 37.186 -39.099 6.129 1.00 0.00 MEMB<br>ATOM 7624 C1C POPE 1 28.000 -30.590 13.390 1.00 0.00 MEMB<br>
ATOM 7627 C1D POPE 1 27.531 -31.928 14.015 1.00 0.00 MEMB<br>ATOM 7630 C1E POPE 1 26.853 -32.876 13.038 1.00 0.00 MEMB<br>ATOM 7633 C1F POPE 1 26.078 -34.112 13.621 1.00 0.00 MEMB<br>
ATOM 7636 C1G POPE 1 25.077 -34.649 12.517 1.00 0.00 MEMB<br>ATOM 7639 C1H POPE 1 23.642 -34.130 12.513 1.00 0.00 MEMB<br>ATOM 7642 C1I POPE 1 22.666 -35.170 11.902 1.00 0.00 MEMB<br>
ATOM 7645 C1J POPE 1 22.744 -35.347 10.415 1.00 0.00 MEMB<br>ATOM 7648 C1K POPE 1 21.584 -36.187 9.891 1.00 0.00 MEMB<br>ATOM 7651 C1L POPE 1 21.250 -35.906 8.447 1.00 0.00 MEMB<br>
ATOM 7654 C1M POPE 1 20.075 -36.745 7.992 1.00 0.00 MEMB<br>ATOM 7657 C1N POPE 1 19.925 -36.586 6.511 1.00 0.00 MEMB<br>ATOM 7660 C1O POPE 1 18.908 -37.540 5.943 1.00 0.00 MEMB<br>
ATOM 7663 C1P POPE 1 18.457 -37.136 4.599 1.00 0.00 MEMB<br><br>
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