[gmx-users] Atomtype CR1 not found
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 16 19:58:45 CEST 2011
rainy908 wrote:
> Hi,
>
> I get the error "Atomtype CR1 not found" when I execute grompp. After perusing the gmx archives, I understand this error has to do with the lack of "CR1" being specified in the force field. However, I did include the appropriate .itp files in my .top file (shown below). As you can see, obviously CR1 is specified in taxol.itp and gtp.itp. Therefore, I'm not sure what exactly is the problem here.
>
You're mixing and matching force fields. PRODRG produces Gromos-compatible
parameters (and does a poor job of that - I can tell you now that the charges
assigned to the aromatic C and H of taxol are total junk). You're then trying
to combine these parameters with OPLS. Even if you could somehow hack the
topology together, the results would be useless.
For more about the hazards of PRODRG, see
http://pubs.acs.org/doi/abs/10.1021/ci100335w.
The solution is to pick a force field and apply it uniformly to the system
you're working with.
-Justin
> Any input on this issue would be greatly appreciated.
>
> 1JFF.top
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ; File '1JFF.top' was generated
> ; By user: onbekend (0)
> ; On host: onbekend
> ; At date: Mon Aug 15 17:22:01 2011
> ;
> ; This is a standalone topology file
> ;
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.5.3
> ;
> ; Command line was:
> ; /software/gromacs/gromacs-4.5.3-x86_64/bin/pdb2gmx -f 1JFF_new.pdb -o 1JFF.gro -p 1JFF.top
> ;
> ; Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "oplsaa.ff/forcefield.itp"
> #include "taxol.itp"
> #include "gdp.itp"
> #include "gtp.itp"
>
> ; Include chain topologies
> #include "1JFF_Protein_chain_A.itp"
> #include "1JFF_Protein_chain_B.itp"
> #include "1JFF_Ion_chain_A2.itp"
>
> ; Include water topology
> #include "oplsaa.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "oplsaa.ff/ions.itp"
>
> [ system ]
> ; Name
> TUBULIN ALPHA CHAIN; TUBULIN BETA CHAIN in water
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Protein_chain_B 1
> Ion_chain_A2 1
> Taxol 1
> GDP 1
> GTP 1
> SOL 21016
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
> taxol.itp
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ; This file was generated by PRODRG version AA081006.0504
> ; PRODRG written/copyrighted by Daan van Aalten
> ; and Alexander Schuettelkopf
> ;
> ; 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.
> ;
> ;
>
> [ moleculetype ]
> ; Name nrexcl
> TA1 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 CR1 1 TA1 C05 1 -0.015 12.0110
> 2 HC 1 TA1 H05 1 0.015 1.0080
> 3 CR1 1 TA1 C06 2 -0.012 12.0110
> 4 HC 1 TA1 H06 2 0.019 1.0080
> 5 CR1 1 TA1 C07 2 -0.012 12.0110
> 6 HC 1 TA1 H07 2 0.019 1.0080
> 7 CR1 1 TA1 C08 2 -0.012 12.0110
> 8 HC 1 TA1 H08 2 0.019 1.0080
> 9 CR1 1 TA1 C09 2 -0.012 12.0110
> 10 HC 1 TA1 H09 2 0.019 1.0080
> 11 C 1 TA1 C04 2 -0.028 12.0110
> 12 C 1 TA1 C03 3 0.357 12.0110
> 13 O 1 TA1 O03 3 -0.710 15.9994
> 14 OA 1 TA1 O02 3 -0.186 15.9994
> 15 CH1 1 TA1 C02 3 0.235 13.0190
> 16 CH1 1 TA1 C10 3 0.148 13.0190
> 17 CH1 1 TA1 C11 3 0.156 12.0110
> 18 OA 1 TA1 O04 4 -0.175 15.9994
> 19 C 1 TA1 C12 4 0.378 12.0110
> 20 O 1 TA1 O05 4 -0.670 15.9994
> ...
> ...
> <snip>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
> gtp.itp
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> [ moleculetype ]
> ; Name nrexcl
> GTP 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 O 1 GTP O6 1 -0.266 15.9994
> 2 C 1 GTP C6 1 0.216 12.0110
> 3 NR 1 GTP N1 1 -0.008 14.0067
> 4 H 1 GTP H1 1 -0.020 1.0080
> 5 C 1 GTP C2 1 0.322 12.0110
> 6 NT 1 GTP N2 1 -0.001 14.0067
> 7 H 1 GTP H22 1 -0.020 1.0080
> 8 H 1 GTP H21 1 -0.020 1.0080
> 9 NR 1 GTP N3 1 -0.203 14.0067
> 10 C 1 GTP C4 2 0.133 12.0110
> 11 C 1 GTP C5 2 0.048 12.0110
> 12 NR 1 GTP N7 2 -0.321 14.0067
> 13 CR1 1 GTP C8 2 -0.037 12.0110
> 14 HC 1 GTP H8 2 -0.019 1.0080
> 15 NR 1 GTP N9 2 0.112 14.0067
> 16 CH1 1 GTP CAU 2 0.084 13.0190
> ..
> ..
> <snip>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
--
========================================
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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