[gmx-users] Capping (neuralising) of peptide
Nuno R. L. Ferreira
nunolf at ci.uc.pt
Thu Sep 30 19:51:34 CEST 2004
----- Original Message -----
From: "Alok" <alokjain at iitk.ac.in>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, September 30, 2004 6:28 PM
Subject: Re: [gmx-users] Capping (neuralising) of peptide
Hello
sorry to bother you again, sir!
I think there is some confusion regarding the simulation that I am doing.
So, I am describing again and it is as follows:
I am trying to simulate four triplet peptides (Gly1-Pro-Gly2).
So, just forget what I said.
I remember someone was asking about multiple peptides, in the e-mail list.
I think that what people uasually do (never done though), is to give a
different chain for each peptide (A, B,C,D for e.g.). In the pdb uploaded
in your previous e-mail, there was no chain id.
Pdb2gmx deals with multiple chains.
I don't know if its better to split your pdb into 4 pieces, one for each
tripeptide and create 4 topologies and merge them afterwards, or to use one
pdb with 4 chains of your peptide.
NUno
I have generated all the four peptides using InsightII and all
the four have different x,y and z coordinates.Also , I have
done the clipping of each peptides (i.e. NH2 in Gly1 and COOH
in Gly2). Then I have generated a pdb file in which all these
peptides are very far away from each other(in the sense of
coordinates).
when i used pdb2gmx -ignh -f peptide.pdb -o peptide.gro -p peptide.top
it genrates .gro and .top file but it also creates the bond between all
four peptides (which i dont want)
So, is there any option in gromacs to keep all these peptides seperately
as different seqments without creating peptide bond between them. (like
the "segment" flag in CHARMM)
I also checked it with pdb2gmx -ignh -ter -f peptide.pdb -o peptide.gro
-p peptide.top but there too, the problem is same.
If I am not wrong then Dr. Peter Tieleman did the same with four
Alamethicin Helices using gromacs.
Kindly suggest me as to what is the alternative and how to proceed further.
Regards,
Alok
output of the pdb2gmx program is as follows:
Opening library file /usr/local/share/gromacs/top/FF.dat
Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3:
OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 64 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 12 residues with 64 atoms
chain #res #atoms
1 ' ' 12 64
All occupancies are one
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb
Back Off! I just backed up peptidetest.top to ./#peptidetest.top.6#
Processing chain 1 (64 atoms, 12 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 20 hydrogen bonds
Checking for duplicate atoms....
deleting duplicate atom O GLY 3 pdb nr 30
deleting duplicate atom O GLY 6 pdb nr 61
deleting duplicate atom O GLY 9 pdb nr 92
deleting duplicate atom O GLY 12 pdb nr 123
Now there are 60 atoms
N-terminus: GLY-NH3+
C-terminus: COO-
Now there are 12 residues with 71 atoms
Making bonds...
Warning: Long Bond (18-20 = 4.40022 nm)
Warning: Long Bond (35-37 = 4.04127 nm)
Warning: Long Bond (52-54 = 4.36763 nm)
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Number of bonds was 79, now 74
Generating angles, dihedrals and pairs...
Before cleaning: 113 pairs
Before cleaning: 133 dihedrals
There are 51 dihedrals, 27 impropers, 107 angles
113 pairs, 74 bonds and 0 dummies
Total mass 862.901 a.m.u.
Total charge 0.000 e
Writing topology
Back Off! I just backed up posre.itp to ./#posre.itp.5#
Writing coordinate file...
Back Off! I just backed up peptide.gro to ./#peptide.gro.4#
--------- PLEASE NOTE ------------
You have succesfully generated a topology from: peptide.pdb.
The select force field and the spc water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
--------- ETON ESAELP ------------
gcq#247: "Uh-oh" (Tinky Winky)
my PDB file :-
REMARK 4
REMARK 4 FINA COMPLIES WITH FORMAT V. 2.0, 30-SEP-2004
ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O GLY 1C 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO GLY 1C 13.391 36.273 29.966 1.00 0.00
H
ATOM 32 N GLY 1 56.800 33.657 40.211 1.00 0.00
N
ATOM 33 CA GLY 1 55.946 34.770 39.811 1.00 0.00
C
ATOM 34 C GLY 1 56.520 36.088 40.276 1.00 0.00
C
ATOM 35 O GLY 1 57.546 36.150 40.944 1.00 0.00
O
ATOM 36 1H GLY 1 57.615 34.017 40.728 1.00 0.00
H
ATOM 37 2H GLY 1 56.269 33.014 40.815 1.00 0.00
H
ATOM 38 1HA GLY 1 55.833 34.791 38.711 1.00 0.00
H
ATOM 39 2HA GLY 1 54.932 34.647 40.234 1.00 0.00
H
ATOM 40 N PRO 1B 55.851 37.165 39.921 1.00 0.00
N
ATOM 41 CA PRO 1B 56.282 38.506 40.283 1.00 0.00
C
ATOM 42 C PRO 1B 56.014 38.808 41.767 1.00 0.00
C
ATOM 43 O PRO 1B 55.036 38.322 42.335 1.00 0.00
O
ATOM 44 CB PRO 1B 55.382 39.378 39.395 1.00 0.00
C
ATOM 45 CG PRO 1B 54.108 38.535 39.232 1.00 0.00
C
ATOM 46 CD PRO 1B 54.642 37.105 39.127 1.00 0.00
C
ATOM 47 HA PRO 1B 57.349 38.632 40.087 1.00 0.00
H
ATOM 48 1HB PRO 1B 55.187 40.363 39.824 1.00 0.00
H
ATOM 49 2HB PRO 1B 55.859 39.502 38.419 1.00 0.00
H
ATOM 50 1HG PRO 1B 53.490 38.628 40.128 1.00 0.00
H
ATOM 51 2HG PRO 1B 53.524 38.823 38.355 1.00 0.00
H
ATOM 52 1HD PRO 1B 53.942 36.372 39.534 1.00 0.00
H
ATOM 53 2HD PRO 1B 54.896 36.856 38.094 1.00 0.00
H
ATOM 54 N GLY 1C 56.838 39.581 42.441 1.00 0.00
N
ATOM 55 CA GLY 1C 56.550 40.015 43.806 1.00 0.00
C
ATOM 56 C GLY 1C 56.089 41.453 43.830 1.00 0.00
C
ATOM 57 O GLY 1C 55.923 42.068 44.883 1.00 0.00
O
ATOM 58 H GLY 1C 57.711 39.892 41.993 1.00 0.00
H
ATOM 59 1HA GLY 1C 55.769 39.375 44.253 1.00 0.00
H
ATOM 60 2HA GLY 1C 57.451 39.913 44.437 1.00 0.00
H
ATOM 61 O GLY 1C 55.849 42.100 42.635 1.00 0.00
O
ATOM 62 HO GLY 1C 55.564 43.000 42.808 1.00 0.00
H
ATOM 63 N GLY 1 51.433 80.760 35.677 1.00 0.00
N
ATOM 64 CA GLY 1 50.640 81.859 35.136 1.00 0.00
C
ATOM 65 C GLY 1 51.130 83.189 35.657 1.00 0.00
C
ATOM 66 O GLY 1 52.047 83.271 36.469 1.00 0.00
O
ATOM 67 1H GLY 1 52.160 81.136 36.303 1.00 0.00
H
ATOM 68 2H GLY 1 50.822 80.123 36.208 1.00 0.00
H
ATOM 69 H GLY 1 50.690 81.860 34.032 1.00 0.00
H
ATOM 70 2HA GLY 1 49.575 81.733 35.408 1.00 0.00
H
ATOM 71 N PRO 1B 50.515 84.254 35.189 1.00 0.00
N
ATOM 72 CA PRO 1B 50.880 85.605 35.587 1.00 0.00
C
ATOM 73 C PRO 1B 50.393 85.929 37.009 1.00 0.00
C
ATOM 74 O PRO 1B 49.345 85.444 37.436 1.00 0.00
O
ATOM 75 CB PRO 1B 50.115 86.454 34.560 1.00 0.00
C
ATOM 76 CG PRO 1B 48.884 85.597 34.226 1.00 0.00
C
ATOM 77 CD PRO 1B 49.437 84.171 34.227 1.00 0.00
C
ATOM 78 HA PRO 1B 51.963 85.737 35.548 1.00 0.00
H
ATOM 79 1HB PRO 1B 49.852 87.444 34.939 1.00 0.00
H
ATOM 80 2HB PRO 1B 50.730 86.566 33.663 1.00 0.00
H
ATOM 81 1HG PRO 1B 48.140 85.700 35.020 1.00 0.00
H
ATOM 82 2HG PRO 1B 48.434 85.866 33.267 1.00 0.00
H
ATOM 83 1HD PRO 1B 48.689 83.438 34.538 1.00 0.00
H
ATOM 84 2HD PRO 1B 49.841 83.907 33.247 1.00 0.00
H
ATOM 85 N GLY 1C 51.104 86.721 37.784 1.00 0.00
N
ATOM 86 CA GLY 1C 50.615 87.174 39.083 1.00 0.00
C
ATOM 87 C GLY 1C 50.147 88.609 39.014 1.00 0.00
C
ATOM 88 O GLY 1C 49.823 89.239 40.019 1.00 0.00
O
ATOM 89 H GLY 1C 52.032 87.032 37.464 1.00 0.00
H
ATOM 90 1HA GLY 1C 49.780 86.535 39.421 1.00 0.00
H
ATOM 91 2HA GLY 1C 51.414 87.090 39.842 1.00 0.00
H
ATOM 92 O GLY 1C 50.081 89.233 37.785 1.00 0.00
O
ATOM 93 HO GLY 1C 49.769 90.133 37.898 1.00 0.00
H
ATOM 94 N GLY 1 11.093 76.967 23.302 1.00 0.00
N
ATOM 95 CA GLY 1 10.300 78.066 22.761 1.00 0.00
C
ATOM 96 C GLY 1 10.791 79.396 23.282 1.00 0.00
C
ATOM 97 O GLY 1 11.708 79.478 24.094 1.00 0.00
O
ATOM 98 1H GLY 1 11.821 77.343 23.928 1.00 0.00
H
ATOM 99 2H GLY 1 10.482 76.330 23.833 1.00 0.00
H
ATOM 100 1HA GLY 1 10.351 78.068 21.657 1.00 0.00
H
ATOM 101 2HA GLY 1 9.236 77.941 23.032 1.00 0.00
H
ATOM 102 N PRO 1B 10.176 80.462 22.814 1.00 0.00
N
ATOM 103 CA PRO 1B 10.540 81.812 23.212 1.00 0.00
C
ATOM 104 C PRO 1B 10.054 82.136 24.634 1.00 0.00
C
ATOM 105 O PRO 1B 9.005 81.651 25.061 1.00 0.00
O
ATOM 106 CB PRO 1B 9.775 82.661 22.185 1.00 0.00
C
ATOM 107 CG PRO 1B 8.544 81.804 21.851 1.00 0.00
C
ATOM 108 CD PRO 1B 9.097 80.378 21.852 1.00 0.00
C
ATOM 109 HA PRO 1B 11.623 81.944 23.173 1.00 0.00
H
ATOM 110 1HB PRO 1B 9.512 83.652 22.564 1.00 0.00
H
ATOM 111 2HB PRO 1B 10.390 82.773 21.288 1.00 0.00
H
ATOM 112 1HG PRO 1B 7.801 81.907 22.645 1.00 0.00
H
ATOM 113 2HG PRO 1B 8.095 82.073 20.892 1.00 0.00
H
ATOM 114 1HD PRO 1B 8.350 79.645 22.163 1.00 0.00
H
ATOM 115 2HD PRO 1B 9.502 80.114 20.872 1.00 0.00
H
ATOM 116 N GLY 1C 10.764 82.928 25.408 1.00 0.00
N
ATOM 117 CA GLY 1C 10.276 83.382 26.708 1.00 0.00
C
ATOM 118 C GLY 1C 9.807 84.816 26.639 1.00 0.00
C
ATOM 119 O GLY 1C 9.483 85.446 27.644 1.00 0.00
O
ATOM 120 H GLY 1C 11.693 83.239 25.089 1.00 0.00
H
ATOM 121 1HA GLY 1C 9.441 82.743 27.046 1.00 0.00
H
ATOM 122 2HA GLY 1C 11.074 83.297 27.467 1.00 0.00
H
ATOM 123 O GLY 1C 9.742 85.440 25.410 1.00 0.00
O
ATOM 124 HO GLY 1C 9.429 86.341 25.523 1.00 0.00
H
END
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