[gmx-users] (no subject)
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 7 20:38:28 CEST 2010
munubas at yahoo.com wrote:
> 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:
>
The atom name is CA, not CH3. The CH3 corresponds to the atom type.
-Justin
> 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
>
>
>
--
========================================
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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