[gmx-users] missing of methyl at N-terminal
Justin A. Lemkul
jalemkul at vt.edu
Fri Nov 7 13:10:02 CET 2008
Bhawana Gupta wrote:
> thankyou for ur reply.
> exact error which i m getting, when running pdb2gmx command with the pdb
> which i had taken from insightII is
> Program pdb2gmx, VERSION 4.0
> Source code file: pdb2gmx.c, line: 429
>
> Fatal error:
> Atom C in residue NH2 6 not found in rtp entry with 3 atoms
> while sorting atoms
>
This probably comes about because you are trying to use parameters from an -NH2
group on a structure that contains -NH(CH3). You also haven't mentioned which
force field you're trying to use. Some force fields do not have an N-methyl
group parameterized (check the .rtp file).
-Justin
>
> this is my pdb in text editor
> there is a presence of 25 atom in my pdb (C in residue NH2 6), but i m
> getting the error mentioned above
> AUTHOR GENERATED BY OPEN BABEL 2.2.0
> ATOM 1 CA ACE 1 -3.811 -0.502 0.471 1.00
> 0.00 C
> ATOM 2 C ACE 1 -2.354 -0.410 0.072 1.00
> 0.00 C
> ATOM 3 O ACE 1 -1.743 -1.403 -0.345 1.00
> 0.00 O
> ATOM 4 N ALA 2 -1.649 0.885 0.183 1.00
> 0.00 N
> ATOM 5 CA ALA 2 -0.244 1.035 -0.187 1.00
> 0.00 C
> ATOM 6 C ALA 2 0.221 2.456 0.023 1.00
> 0.00 C
> ATOM 7 O ALA 2 -0.530 3.334 0.466 1.00
> 0.00 O
> ATOM 8 CB ALA 2 -0.094 0.568 -1.645 1.00
> 0.00 C
> ATOM 9 N ALA 3 1.482 2.703 -0.281 1.00
> 0.00 N
> ATOM 10 CA ALA 3 2.069 4.031 -0.129 1.00
> 0.00 C
> ATOM 11 C ALA 3 3.519 4.033 -0.548 1.00
> 0.00 C
> ATOM 12 O ALA 3 4.081 3.015 -0.969 1.00
> 0.00 O
> ATOM 13 CB ALA 3 1.870 4.463 1.334 1.00
> 0.00 C
> ATOM 14 N ALA 4 4.149 5.189 -0.449 1.00
> 0.00 N
> ATOM 15 CA ALA 4 5.553 5.340 -0.819 1.00
> 0.00 C
> ATOM 16 C ALA 4 6.019 6.761 -0.609 1.00
> 0.00 C
> ATOM 17 O ALA 4 5.267 7.638 -0.166 1.00
> 0.00 O
> ATOM 18 CB ALA 4 5.704 4.872 -2.277 1.00
> 0.00 C
> ATOM 19 N ALA 5 7.279 7.008 -0.913 1.00
> 0.00 N
> ATOM 20 CA ALA 5 7.866 8.336 -0.760 1.00
> 0.00 C
> ATOM 21 C ALA 5 9.317 8.337 -1.179 1.00
> 0.00 C
> ATOM 22 O ALA 5 9.879 7.319 -1.601 1.00
> 0.00 O
> ATOM 23 CB ALA 5 7.668 8.768 0.703 1.00
> 0.00 C
> ATOM 24 N NHM 6 10.022 9.633 -1.069 1.00
> 0.00 N
> ATOM 25 C NHM 6 11.417 9.736 -1.462 1.00
> 0.00 C
> CONECT 1 2
> CONECT 2 3 4 1
> CONECT 3 2
> CONECT 4 5 2
> CONECT 5 8 6 4
> CONECT 6 9 5 7
> CONECT 7 6
> CONECT 8 5
> CONECT 9 10 6
> CONECT 10 11 9 13
> CONECT 11 12 14 10
> CONECT 12 11
> CONECT 13 10
> CONECT 14 15 11
> CONECT 15 18 16 14
> CONECT 16 19 15 17
> CONECT 17 16
> CONECT 18 15
> CONECT 19 20 16
> CONECT 20 21 19 23
> CONECT 21 22 24 20
> CONECT 22 21
> CONECT 23 20
> CONECT 24 25 21
> CONECT 25 24
> MASTER 0 0 0 0 0 0 0 0 25 0 25 0
> END
>
> Please help me out.
>
> With regards
> Bhawana
>
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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