Hi Neha, Yes. The MN* particles are the virtual sites.
Cheers, Tsjerk On Wed, Sep 18, 2013 at 7:13 AM, Neha Gandhi <n.gandh...@gmail.com> wrote: > Dear Users, > > I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am > using following command. > pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -ignh > > Upon visualisation I could see triangle like sites. Does the output seem > right? > > 75 > 1VAL MN1 1 2.913 3.551 3.288 > 1VAL MN2 2 2.880 3.575 3.356 > 1VAL N 3 2.891 3.561 3.320 > 1VAL H1 4 2.960 3.543 3.250 > 1VAL H2 5 2.887 3.659 3.339 > 1VAL H3 6 2.915 3.511 3.403 > 1VAL CA 7 2.758 3.515 3.271 > 1VAL CB 8 2.761 3.365 3.234 > 1VAL CG1 9 2.628 3.322 3.174 > 1VAL CG2 10 2.878 3.334 3.138 > 1VAL C 11 2.651 3.542 3.379 > 1VAL O 12 2.640 3.469 3.476 > 2GLN N 13 2.578 3.652 3.361 > 2GLN H 14 2.599 3.711 3.283 > 2GLN CA 15 2.467 3.691 3.449 > 2GLN CB 16 2.497 3.826 3.515 > 2GLN CG 17 2.399 3.863 3.627 > 2GLN CD 18 2.427 3.999 3.688 > 2GLN OE1 19 2.428 4.101 3.617 > 2GLN NE2 20 2.450 4.003 3.818 > 2GLN HE21 21 2.449 3.918 3.872 > 2GLN HE22 22 2.469 4.090 3.863 > 2GLN C 23 2.342 3.700 3.363 > 2GLN O 24 2.337 3.777 3.269 > 3ILE N 25 2.242 3.620 3.396 > 3ILE H 26 2.250 3.564 3.479 > 3ILE CA 27 2.119 3.610 3.317 > 3ILE CB 28 2.107 3.470 3.251 > 3ILE CG1 29 2.228 3.440 3.162 > 3ILE CG2 30 1.981 3.459 3.168 > 3ILE CD 31 2.257 3.295 3.151 > 3ILE C 32 2.000 3.634 3.409 > 3ILE O 33 1.985 3.563 3.508 > 4VAL N 34 1.918 3.734 3.379 > 4VAL H 35 1.936 3.789 3.297 > 4VAL CA 36 1.802 3.766 3.463 > 4VAL CB 37 1.817 3.903 3.533 > 4VAL CG1 38 1.695 3.934 3.619 > 4VAL CG2 39 1.944 3.903 3.618 > 4VAL C 40 1.674 3.766 3.381 > 4VAL O 41 1.664 3.838 3.283 > 5TYR N 42 1.580 3.682 3.422 > 5TYR H 43 1.602 3.617 3.494 > 5TYR CA 44 1.445 3.681 3.366 > 5TYR CB 45 1.400 3.537 3.337 > 5TYR CG 46 1.463 3.471 3.217 > 5TYR CD1 47 1.572 3.386 3.230 > 5TYR HD1 48 1.610 3.368 3.321 > 5TYR CD2 49 1.413 3.494 3.089 > 5TYR HD2 50 1.334 3.555 3.077 > 5TYR CE1 51 1.629 3.326 3.120 > 5TYR HE1 52 1.707 3.264 3.131 > 5TYR CE2 53 1.469 3.434 2.978 > 5TYR HE2 54 1.431 3.451 2.887 > 5TYR CZ 55 1.578 3.351 2.993 > 5TYR OH 56 1.632 3.291 2.882 > 5TYR HH 57 1.582 3.321 2.800 > 5TYR C 58 1.352 3.741 3.471 > 5TYR O 59 1.337 3.685 3.580 > 6LYS N 60 1.290 3.853 3.439 > 6LYS H 61 1.306 3.895 3.349 > 6LYS CA 62 1.197 3.917 3.532 > 6LYS CB 63 1.271 4.015 3.624 > 6LYS CG 64 1.323 4.142 3.559 > 6LYS CD 65 1.428 4.211 3.649 > 6LYS CE 66 1.468 4.349 3.597 > 6LYS MNZ1 67 1.590 4.442 3.650 > 6LYS MNZ2 68 1.594 4.377 3.696 > 6LYS NZ 69 1.587 4.407 3.670 > 6LYS HZ1 70 1.608 4.497 3.632 > 6LYS HZ2 71 1.565 4.416 3.767 > 6LYS HZ3 72 1.665 4.346 3.659 > 6LYS C 73 1.080 3.982 3.461 > 6LYS O1 74 1.065 3.973 3.340 > 6LYS O2 75 0.988 4.044 3.539 > > -- > Regards, > Dr. Neha S. Gandhi, > Curtin Research Fellow, > School of Biomedical Sciences, > Curtin University, > Perth GPO U1987 > Australia > LinkedIn > Research Gate > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
