[gmx-users] Fatal error: Atomtype 'OS' not found!
David van der Spoel
spoel at xray.bmc.uu.se
Thu Oct 7 09:08:00 CEST 2004
On Thu, 2004-10-07 at 00:27, Yunfeng Hu wrote:
> However, everything is fine if cocaine.itp alone without protein is
> used in the simulation. Here is what it looks like:
ffG43a1 has no atomtype OS. So this itp file can not work with that ff.
Check earlier discussions of prodrg and ffG43 on the list.
>
> [ moleculetype ]
> ;name nrexcl
> COC 3
> ;
> ;
> ; This file was generated by PRODRG version 040913.0519
> ; PRODRG written/copyrighted by Daan van Aalten
> ;
> ; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> ;
> ; When using this software in a publication, cite:
> ; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> ; PRODRG - a tool for high-throughput crystallography
> ; of protein-ligand complexes.
> ; Acta Crystallogr. D60, 1355--1363.
> ;
> ;
> [ atoms ]
> ; nr type resnr resid atom cgnr charge
> 1 CH3 1 COC C1 1 0.078
> 2 OS 1 COC O5 1 -0.110
> 3 C 1 COC C6 1 0.531
> 4 O 1 COC O7 1 -0.499
> 5 CH1 1 COC C8 2 0.127
> 6 CH1 1 COC C10 2 0.127
> 7 NL 1 COC N12 2 -0.300
> 8 CH3 1 COC C14 2 0.046
> 9 CH2 1 COC C18 3 0.000
> 10 CH2 1 COC C21 3 0.000
> 11 CH1 1 COC C24 4 0.000
> 12 CH2 1 COC C26 5 0.100
> 13 CS1 1 COC C29 5 0.258
> 14 OS 1 COC O1 5 -0.141
> 15 C 1 COC C2 5 0.418
> 16 O 1 COC O3 5 -0.635
> 17 CB 1 COC C4 6 0.015
> 18 CR61 1 COC C5 6 -0.007
> 19 CR61 1 COC C7 6 -0.008
> 20 CR61 1 COC C9 7 0.000
> 21 CR61 1 COC C11 7 0.000
> 22 CR61 1 COC C13 7 0.000
> [ bonds ]
> ;ai aj fu c0 c1
> 1 2 1 0.143 251040.0 0.143 251040.0 ; C1 O5
> 2 3 1 0.136 376560.0 0.136 376560.0 ; O5 C6
> 3 4 1 0.123 502080.0 0.123 502080.0 ; C6 O7
> 3 5 1 0.153 334720.0 0.153 334720.0 ; C6 C8
> 5 6 1 0.153 334720.0 0.153 334720.0 ; C8 C10
> 5 13 1 0.153 334720.0 0.153 334720.0 ; C8 C29
> 6 7 1 0.147 376560.0 0.147 376560.0 ; C10 N12
> 6 9 1 0.153 334720.0 0.153 334720.0 ; C10 C18
> 7 8 1 0.147 376560.0 0.147 376560.0 ; N12 C14
> 7 11 1 0.147 376560.0 0.147 376560.0 ; N12 C24
> 9 10 1 0.153 334720.0 0.153 334720.0 ; C18 C21
> 10 11 1 0.153 334720.0 0.153 334720.0 ; C21 C24
> 11 12 1 0.153 334720.0 0.153 334720.0 ; C24 C26
> 12 13 1 0.153 251040.0 0.153 251040.0 ; C26 C29
> 13 14 1 0.144 251040.0 0.144 251040.0 ; C29 O1
> 14 15 1 0.136 376560.0 0.136 376560.0 ; O1 C2
> 15 16 1 0.123 502080.0 0.123 502080.0 ; C2 O3
> 15 17 1 0.153 334720.0 0.153 334720.0 ; C2 C4
> 17 18 1 0.139 418400.0 0.139 418400.0 ; C4 C5
> 17 22 1 0.139 418400.0 0.139 418400.0 ; C4 C13
> 18 19 1 0.139 418400.0 0.139 418400.0 ; C5 C7
> 19 20 1 0.139 418400.0 0.139 418400.0 ; C7 C9
> 20 21 1 0.139 418400.0 0.139 418400.0 ; C9 C11
> 21 22 1 0.139 418400.0 0.139 418400.0 ; C11 C13
> [ pairs ]
> ;ai aj fu c0 c1
> 1 4 1 ; C1 O7
> 1 5 1 ; C1 C8
> 2 6 1 ; O5 C10
> 2 13 1 ; O5 C29
> 3 7 1 ; C6 N12
> 3 9 1 ; C6 C18
> 3 12 1 ; C6 C26
> 3 14 1 ; C6 O1
> 4 6 1 ; O7 C10
> 4 13 1 ; O7 C29
> 5 8 1 ; C8 C14
> 5 10 1 ; C8 C21
> 5 11 1 ; C8 C24
> 5 15 1 ; C8 C2
> 6 12 1 ; C10 C26
> 6 14 1 ; C10 O1
> 7 13 1 ; N12 C29
> 8 9 1 ; C14 C18
> 8 10 1 ; C14 C21
> 8 12 1 ; C14 C26
> 9 12 1 ; C18 C26
> 9 13 1 ; C18 C29
> 10 13 1 ; C21 C29
> 11 14 1 ; C24 O1
> 12 15 1 ; C26 C2
> 13 16 1 ; C29 O3
> 13 17 1 ; C29 C4
> 14 18 1 ; O1 C5
> 14 22 1 ; O1 C13
> 15 19 1 ; C2 C7
> 15 21 1 ; C2 C11
> 16 18 1 ; O3 C5
> 16 22 1 ; O3 C13
> 17 20 1 ; C4 C9
> 18 21 1 ; C5 C11
> 19 22 1 ; C7 C13
> [ angles ]
> ;ai aj ak fu c0 c1
> 1 2 3 1 109.5 334.7 109.5 334.7 ; C1 O5 C6
> 2 3 4 1 120.0 418.4 120.0 418.4 ; O5 C6 O7
> 2 3 5 1 120.0 418.4 120.0 418.4 ; O5 C6 C8
> 4 3 5 1 121.0 502.1 121.0 502.1 ; O7 C6 C8
> 3 5 6 1 109.5 460.2 109.5 460.2 ; C6 C8 C10
> 3 5 13 1 109.5 460.2 109.5 460.2 ; C6 C8 C29
> 6 5 13 1 111.0 460.2 111.0 460.2 ; C10 C8 C29
> 5 6 7 1 109.5 460.2 109.5 460.2 ; C8 C10 N12
> 5 6 9 1 111.0 460.2 111.0 460.2 ; C8 C10 C18
> 7 6 9 1 104.0 460.2 104.0 460.2 ; N12 C10 C18
> 6 7 8 1 109.5 376.6 109.5 376.6 ; C10 N12 C14
> 6 7 11 1 104.0 460.2 104.0 460.2 ; C10 N12 C24
> 8 7 11 1 109.5 376.6 109.5 376.6 ; C14 N12 C24
> 6 9 10 1 104.0 460.2 104.0 460.2 ; C10 C18 C21
> 9 10 11 1 104.0 460.2 104.0 460.2 ; C18 C21 C24
> 7 11 10 1 104.0 460.2 104.0 460.2 ; N12 C24 C21
> 7 11 12 1 109.5 460.2 109.5 460.2 ; N12 C24 C26
> 10 11 12 1 109.5 460.2 109.5 460.2 ; C21 C24 C26
> 11 12 13 1 109.5 460.2 109.5 460.2 ; C24 C26 C29
> 5 13 12 1 109.5 251.0 109.5 251.0 ; C8 C29 C26
> 5 13 14 1 109.5 284.5 109.5 284.5 ; C8 C29 O1
> 12 13 14 1 109.5 284.5 109.5 284.5 ; C26 C29 O1
> 13 14 15 1 109.5 334.7 109.5 334.7 ; C29 O1 C2
> 14 15 16 1 120.0 418.4 120.0 418.4 ; O1 C2 O3
> 14 15 17 1 120.0 418.4 120.0 418.4 ; O1 C2 C4
> 16 15 17 1 121.0 502.1 121.0 502.1 ; O3 C2 C4
> 15 17 18 1 120.0 418.4 120.0 418.4 ; C2 C4 C5
> 15 17 22 1 120.0 418.4 120.0 418.4 ; C2 C4 C13
> 18 17 22 1 120.0 418.4 120.0 418.4 ; C5 C4 C13
> 17 18 19 1 120.0 418.4 120.0 418.4 ; C4 C5 C7
> 18 19 20 1 120.0 418.4 120.0 418.4 ; C5 C7 C9
> 19 20 21 1 120.0 418.4 120.0 418.4 ; C7 C9 C11
> 20 21 22 1 120.0 418.4 120.0 418.4 ; C9 C11 C13
> 17 22 21 1 120.0 418.4 120.0 418.4 ; C4 C13 C11
> [ dihedrals ]
> ;ai aj ak al fu c0 c1 m c0 c1 m
> 3 2 5 4 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C6 O5
> C8 O7
> 15 14 17 16 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C2 O1
> C4 O3
> 17 22 18 15 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C4 C13
> C5 C2
> 5 3 6 13 2 35.3 836.8 0 35.3 836.8 0 ; IDI C8 C6
> C10 C29
> 6 5 7 9 2 35.3 836.8 0 35.3 836.8 0 ; IDI C10 C8
> N12 C18
> 7 6 11 8 2 35.3 836.8 0 35.3 836.8 0 ; IDI N12 C10
> C24 C14
> 11 7 12 10 2 35.3 836.8 0 35.3 836.8 0 ; IDI C24 N12
> C26 C21
> 13 5 12 14 2 35.3 836.8 0 35.3 836.8 0 ; IDI C29 C8
> C26 O1
> 17 18 19 20 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C4 C5
> C7 C9
> 18 19 20 21 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C5 C7
> C9 C11
> 19 20 21 22 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C7 C9
> C11 C13
> 20 21 22 17 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C9 C11
> C13 C4
> 21 22 17 18 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C11 C13
> C4 C5
> 22 17 18 19 2 0.0 1673.6 0 0.0 1673.6 0 ; IDI C13 C4
> C5 C7
> 1 2 3 5 1 180.0 16.7 2 180.0 16.7 2 ; DI C1 O5
> C6 C8
> 13 5 3 2 1 0.0 0.4 6 0.0 0.4 6 ; DI C29 C8
> C6 O5
> 9 6 5 3 1 0.0 5.9 3 0.0 5.9 3 ; DI C18 C10
> C8 C6
> 3 5 13 14 1 0.0 5.9 3 0.0 5.9 3 ; DI C6 C8
> C29 O1
> 5 6 7 11 1 0.0 3.8 3 0.0 3.8 3 ; DI C8 C10
> N12 C24
> 10 9 6 5 1 0.0 5.9 3 0.0 5.9 3 ; DI C21 C18
> C10 C8
> 12 11 7 6 1 0.0 3.8 3 0.0 3.8 3 ; DI C26 C24
> N12 C10
> 11 10 9 6 1 0.0 5.9 3 0.0 5.9 3 ; DI C24 C21
> C18 C10
> 9 10 11 12 1 0.0 5.9 3 0.0 5.9 3 ; DI C18 C21
> C24 C26
> 13 12 11 7 1 0.0 5.9 3 0.0 5.9 3 ; DI C29 C26
> C24 N12
> 14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; DI O1 C29
> C26 C24
> 5 13 14 15 1 0.0 3.8 3 0.0 3.8 3 ; DI C8 C29
> O1 C2
> 13 14 15 17 1 180.0 16.7 2 180.0 16.7 2 ; DI C29 O1
> C2 C4
> 22 17 15 14 1 180.0 5.9 2 180.0 5.9 2 ; DI C13 C4
> C2 O1
>
>
> On Wed, 2004-10-06 at 18:49, Yunfeng Hu wrote:
> > In fact that is what I did. Here is what my topology file looks like:
> > ;
> > ; File '7a1.top' was generated
> > ; By user: yunfenghu (501)
> > ; On host: Yunfeng-Hus-Computer.local
> > ; At date: Thu Sep 30 17:46:23 2004
> > ;
> > ; This is your topology file
> > ; "Uh-oh .... Right Again" (Laurie Anderson)
> > ;
> > ; Include forcefield parameters
> > #include "ffG43a1.itp"
> > #include "cocaine.itp"
>
> Most likely your file cocaine.tip also includes a forcefield statement
> and/or atomtypes and/or charges in cocaine.itp have to be adapted to
> ffG43a1 (which are different than ffgmx).
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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