[gmx-users] (no subject)

Wed Jul 7 20:35:39 CEST 2010

Hi,
I am using GROMACS 4.0 for simulating a peptide having 5 residues.  I have built the sequence using pymol and capped the peptide with CH3CO and NHCH3 at its N and C terminal respectively and save in pdb file format.  The pdb file was used to produce *.gro and *.top files using pdb2gmx ff G43a1 -ignh  -f *.pdb -o *.gro -p *.top -ter.  It has shown the option NH3+, NH2 and None.  When choosing "None" it flashes error as well as not producing required files i.e. *.top and *.gro.  Gromacs has library on NH3+, NH2, None and COO-, COOH, None at N and C terminal respectively.  I have opened the file ff G43a1.rtp and I included the option CH3.  Accordingly I have included in the files such as ffG43a1-n.tdb, ffG43a1-c.tdb, ffgmx.rtp, ffgmx-n.tdb and ffgmx-c.tdb which are responsible for making *.gro and *.top files.  It flashes error the the atom CH3  in rsidue ACE  1 not found in rtp entry with 3 atoms while sorting atoms.  Due to this I could
 not proceed further for simulating the peptides.  The input *.pdb files is as:

ATOM 1        C         ACE 1       -1.453       -2.461       -2.313      1.00   0.00      C
ATOM 2        O         ACE 1       -1.746      -1.409       -2.895       1.00   0.00      O
ATOM 3       CH3      ACE 1       -2.252       -3.727      -2.539       1.00   0.00      C
ATOM 4     1HH3      ACE 1       -2.215       -4.006      -3.582       1.00   0.00      H
ATOM 5     2HH3      ACE 1       -1.844       -4.532      -1.947       1.00   0.00      H
ATOM 6     3HH3      ACE 1       -3.281       -3.569      -2.255       1.00   0.00      H
ATOM 7       N          GLN 2       -0.311       -2.482      -1.387       1.00   0.00     N
ATOM 8       CA        GLN 2       0.241        -1.131      -1.387       1.00   0.00     C
ATOM 9       C          GLN 2       1.751        -1.162      -1.387       1.00   0.00     C
ATOM 10     O          GLN 2       2.386        -1.913      -0.650       1.00   0.00     O
ATOM 11     CB        GLN 2      -0.297        -0.376      -0.151       1.00   0.00     C
ATOM 12     CG        GLN 2      0.152          1.115     -0.003        1.00   0.00     C
ATOM 13     CD        GLN 2      -0.293         1.910      1.231        1.00   0.00     C
ATOM 14     NE2      GLN 2      -1.052         1.345      2.135        1.00   0.00     N
ATOM 15     OE1      GLN 2       0.069         3.064      1.402        1.00   0.00     O
ATOM 16     H          GLN 2       0.008        -3.235     -0.883        1.00   0.00     H
ATOM 17     HA        GLN 2      -0.083        -0.615     -2.310        1.00   0.00     H
ATOM 18     2HB      GLN 2       0.002        -0.934      0.761        1.00   0.00     H
ATOM 19     3HB      GLN 2      -1.404        -0.411     -0.164        1.00   0.00     H
ATOM 20     2HG      GLN 2      -0.150         1.693     -0.896        1.00   0.00     H
ATOM 21    3HG       GLN 2       1.255         1.185      0.008        1.00   0.00     H
ATOM 22    1HE2     GLN 2       -1.249         1.921       2.955       1.00   0.00    H
ATOM 23    2HE2     GLN 2       -1.262         0.359      1.967        1.00   0.00    H
ATOM 24      N         GLN 3       2.483         -0.268      -2.296       1.00   0.00    N
ATOM 25 CA GLN 3 3.901 -0.525 -2.069 1.00 0.00 C
ATOM 26 C GLN 3 4.691 0.763 -2.064 1.00 0.00 C
ATOM 27 O GLN 3 4.517 1.636 -2.911 1.00 0.00 O
ATOM 28 CB GLN 3 4.413 -1.484 -3.166 1.00 0.00 C
ATOM 29 CG GLN 3 5.913 -1.914 -3.062 1.00 0.00 C
ATOM 30 CD GLN 3 6.509 -2.817 -4.150 1.00 0.00 C
ATOM 31 NE2 GLN 3 5.759 -3.230 -5.140 1.00 0.00 N
ATOM 32 OE1 GLN 3 7.686 -3.143 -4.125 1.00 0.00 O
ATOM 33 H GLN 3 2.103 0.360 -2.916 1.00 0.00 H
ATOM 34 HA GLN 3 4.022 -0.995 -1.075 1.00 0.00 H
ATOM 35 2HB GLN 3 4.242 -1.011 -4.156 1.00 0.00 H
ATOM 36 3HB GLN 3 3.784 -2.396 -3.166 1.00 0.00 H
ATOM 37 2HG GLN 3 6.102 -2.402 -2.088 1.00 0.00 H
ATOM 38 3HG GLN 3 6.569 -1.025 -3.054 1.00 0.00 H
ATOM 39 1HE2 GLN 3 6.248 -3.772 -5.855 1.00 0.00 H
ATOM 40 2HE2 GLN 3 4.804 -2.867 -5.139 1.00 0.00 H
ATOM 41 N GLN 4 5.698 0.978 -1.015 1.00 0.00 N
ATOM 42 CA GLN 4 6.284 2.289 -1.272 1.00 0.00 C
ATOM 43 C GLN 4 7.779 2.267 -1.059 1.00 0.00 C
ATOM 44 O GLN 4 8.372 1.247 -0.713 1.00 0.00 O
ATOM 45 CB GLN 4 5.608 3.324 -0.346 1.00 0.00 C
ATOM 46 CG GLN 4 6.077 4.808 -0.510 1.00 0.00 C
ATOM 47 CD GLN 4 5.494 5.882 0.418 1.00 0.00 C
ATOM 48 NE2 GLN 4 4.606 5.555 1.321 1.00 0.00 N
ATOM 49 OE1 GLN 4 5.864 7.044 0.347 1.00 0.00 O
ATOM 50 H GLN 4 5.925 0.375 -0.302 1.00 0.00 H
ATOM 51 HA GLN 4 6.102 2.559 -2.329 1.00 0.00 H
ATOM 52 2HB GLN 4 5.767 3.012 0.708 1.00 0.00 H
ATOM 53 3HB GLN 4 4.513 3.282 -0.501 1.00 0.00 H
ATOM 54 2HG GLN 4 5.914 5.145 -1.550 1.00 0.00 H
ATOM 55 3HG GLN 4 7.170 4.884 -0.366 1.00 0.00 H
ATOM 56 1HE2 GLN 4 4.318 6.315 1.939 1.00 0.00 H
ATOM 57 2HE2 GLN 4 4.391 4.557 1.374 1.00 0.00 H
ATOM 58 N NME 5 8.549 3.501 -1.271 1.00 0.00 N
ATOM 59 CH3 NME 5 9.939 3.182 -0.995 1.00 0.00 C
ATOM 60 H NME 5 8.174 4.416 -1.559 1.00 0.00 H
ATOM 61 1HH3 NME 5 9.998 2.334 -0.330 1.00 0.00 H
ATOM 62 2HH3 NME 5 10.453 2.943 -1.915 1.00 0.00 H
ATOM 63 3HH3 NME 5 10.426 4.027 -0.530 1.00 0.00 H
END

The topology file is as

;
; File 'gln/gln.top' was generated
; By user: root (0)
; On host: linux-g5pu
; At date: Sat Mar 8 05:19:11 1980
;
; This is your topology file
; "Lets Kill the Fucking Band" (Tom Savini - From Dusk til Dawn) 
;
; Include forcefield parameters
#include "ffG43a1.itp"

Please suggest me to overcome this problem as to what I have to do.

M. Baskar

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