[gmx-users] Proline on OPLSSaa
Mauro Puppett
esagono at hotmail.com
Mon Feb 18 16:53:14 CET 2008
-----------------------------
Sorry but I'm not able to solve the problem.
I've added the impropers for ACE and PRO but I still have warnings.
Checking the lines, the warning refers to the dihedrals of the methoxy group. I'm not able to find anywhere how to fix this problem.
Could you please help me again?
Thanks
> Date: Mon, 11 Feb 2008 09:16:16 +0100
> From: tsjerkw at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Proline on OPLSSaa
>
> Hi Mauro,
>
> The .top says it all: you haven't specified parameters. Just listing
> the bonds, angles and dihedrals in the .rtp file is not enough. You'll
> have to assign parameters to them. Check the entries (notably PRO and
> ACE) in the .rtp file of your choice...
>
> Cheers,
>
> Tsjerk
>
> On Feb 11, 2008 12:02 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > Mauro Puppett wrote:
> > >
> > > Hi all,
> > > I'm trying to run a simulation of a proline in water tip5p with OPLSaa ff.
> >
> > <snip>
> >
> > > and it works fine till i run grompp which says:
> > >
> > > ERROR 0 [file "proline.top", line 182]:
> > > No default Ryckaert-Bell. types
> > > ERROR 0 [file "proline.top", line 191]:
> > > No default Ryckaert-Bell. types
> > > ERROR 0 [file "proline.top", line 193]:
> > > No default Ryckaert-Bell. types
> > > ERROR 0 [file "proline.top", line 201]:
> > > No default Ryckaert-Bell. types
> >
> > Well, what's on these lines? Probably you're mis-naming some atom types,
> > but you'll need to do your own leg-work finding out which ones!
> >
> > Mark
> >
> >
> > > This is my .top file:
> > >
> > > ; This is your topology file
> > > ; %E
> > > ;
> > > ; Include forcefield parameters
> > > #include "ffoplsaa.itp"
> > >
> > > ; Include water topology
> > > #include "tip5p.itp"
> > >
> > > #ifdef POSRES_WATER
> > > ; Position restraint for each water oxygen
> > > [ position_restraints ]
> > > ; i funct fcx fcy fcz
> > > 1 1 1000 1000 1000
> > > #endif
> > >
> > >
> > > [ moleculetype ]
> > > ; Name nrexcl
> > > Protein 3
> > >
> > > [ atoms ]
> > > ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> > > 1 opls_239 1 APR N 1 -0.776797 14.0067 ; qtot -0.7768
> > > 2 opls_246 1 APR CA 2 -0.158578 12.011 ; qtot -0.9354
> > > 3 opls_058 1 APR C1 3 0.95425 12.011 ; qtot 0.01887
> > > 4 opls_062 1 APR OS1 4 -0.71999 15.9994 ; qtot -0.7011
> > > 5 opls_235 1 APR C2 5 0.808979 12.011 ; qtot 0.1079
> > > 6 opls_059 1 APR OS 6 -0.616492 15.9994 ; qtot -0.5086
> > > 7 opls_245 1 APR CD 7 -0.150278 12.011 ; qtot -0.6589
> > > 8 opls_136 1 APR CB 8 -0.404838 12.011 ; qtot -1.064
> > > 9 opls_140 1 APR HB1 9 0.24345 1.008 ; qtot -0.8203
> > > 10 opls_136 1 APR CG 10 -0.450709 12.011 ; qtot -1.271
> > > 11 opls_140 1 APR HB2 11 0.226125 1.008 ; qtot -1.045
> > > 12 opls_140 1 APR HG1 12 0.223126 1.008 ; qtot -0.8218
> > > 13 opls_140 1 APR HG2 13 0.242534 1.008 ; qtot -0.5792
> > > 14 opls_140 1 APR HD1 14 0.23943 1.008 ; qtot -0.3398
> > > 15 opls_140 1 APR HD2 15 0.239331 1.008 ; qtot -0.1005
> > > 16 opls_140 1 APR HA 16 0.262623 1.008 ; qtot 0.1622
> > > 17 opls_468 1 APR CE 17 -0.252649 12.011 ; qtot -0.09048
> > > 18 opls_469 1 APR HE1 18 0.216104 1.008 ; qtot 0.1256
> > > 19 opls_469 1 APR HE2 19 0.214466 1.008 ; qtot 0.3401
> > > 20 opls_469 1 APR HE3 20 0.212312 1.008 ; qtot 0.5524
> > > 21 opls_236 1 APR OB 21 -0.606932 15.9994 ; qtot -0.05453
> > > 22 opls_135 1 APR CF 22 -0.687405 12.011 ; qtot -0.7419
> > > 23 opls_140 1 APR HF1 23 0.262125 1.008 ; qtot -0.4798
> > > 24 opls_140 1 APR HF2 24 0.224449 1.008 ; qtot -0.2554
> > > 25 opls_140 1 APR HF3 25 0.255303 1.008 ; qtot -6.101e-05
> > >
> > > [ bonds ]
> > > ; ai aj funct c0 c1 c2 c3
> > > 1 2 1
> > > 1 5 1
> > > 1 7 1
> > > 2 3 1
> > > 2 8 1
> > > 3 4 1
> > > 3 6 1
> > > 4 17 1
> > > 5 21 1
> > > 5 22 1
> > > 7 10 1
> > > 7 14 1
> > > 7 15 1
> > > 8 9 1
> > > 8 10 1
> > > 8 11 1
> > > 10 12 1
> > > 10 13 1
> > > 17 18 1
> > > 17 20 1
> > > 22 23 1
> > > 22 24 1
> > > 22 25 1
> > >
> > > [ pairs ]
> > > ; ai aj funct c0 c1 c2 c3
> > > 1 4 1
> > > 1 6 1
> > > 1 9 1
> > > 1 11 1
> > > 1 12 1
> > > 1 13 1
> > > 1 23 1
> > > 1 24 1
> > > 1 25 1
> > > 2 12 1
> > > 2 13 1
> > > 2 14 1
> > > 2 15 1
> > > 2 17 1
> > > 2 21 1
> > > 2 22 1
> > > 3 5 1
> > > 3 7 1
> > > 3 9 1
> > > 3 10 1
> > > 3 11 1
> > > 3 18 1
> > > 3 20 1
> > > 4 8 1
> > > 5 8 1
> > > 5 10 1
> > > 5 14 1
> > > 5 15 1
> > > 6 8 1
> > > 6 17 1
> > > 7 9 1
> > > 7 11 1
> > > 7 21 1
> > > 7 22 1
> > > 8 14 1
> > > 8 15 1
> > > 9 12 1
> > > 9 13 1
> > > 11 12 1
> > > 11 13 1
> > > 12 14 1
> > > 12 15 1
> > > 13 14 1
> > > 13 15 1
> > > 21 23 1
> > > 21 24 1
> > > 21 25 1
> > >
> > > [ angles ]
> > > ; ai aj ak funct c0 c1 c2 c3
> > > 2 1 5 1
> > > 2 1 7 1
> > > 5 1 7 1
> > > 1 2 3 1
> > > 1 2 8 1
> > > 3 2 8 1
> > > 2 3 4 1
> > > 2 3 6 1
> > > 4 3 6 1
> > > 3 4 17 1
> > > 1 5 21 1
> > > 1 5 22 1
> > > 21 5 22 1
> > > 1 7 10 1
> > > 1 7 14 1
> > > 1 7 15 1
> > > 10 7 14 1
> > > 10 7 15 1
> > > 14 7 15 1
> > > 2 8 9 1
> > > 2 8 10 1
> > > 2 8 11 1
> > > 9 8 10 1
> > > 9 8 11 1
> > > 10 8 11 1
> > > 7 10 8 1
> > > 7 10 12 1
> > > 7 10 13 1
> > > 8 10 12 1
> > > 8 10 13 1
> > > 12 10 13 1
> > > 4 17 18 1
> > > 4 17 20 1
> > > 18 17 20 1
> > > 5 22 23 1
> > > 5 22 24 1
> > > 5 22 25 1
> > > 23 22 24 1
> > > 23 22 25 1
> > > 24 22 25 1
> > >
> > > [ dihedrals ]
> > > ; ai aj ak al funct c0 c1 c2 c3 c4 c5
> > > 5 1 2 3 3
> > > 5 1 2 8 3
> > > 7 1 2 3 3
> > > 7 1 2 8 3
> > > 2 1 5 21 3
> > > 2 1 5 22 3
> > > 7 1 5 21 3
> > > 7 1 5 22 3
> > > 2 1 7 10 3
> > > 2 1 7 14 3
> > > 2 1 7 15 3
> > > 5 1 7 10 3
> > > 5 1 7 14 3
> > > 5 1 7 15 3
> > > 1 2 3 4 3
> > > 1 2 3 6 3
> > > 8 2 3 4 3
> > > 8 2 3 6 3
> > > 1 2 8 9 3
> > > 1 2 8 10 3
> > > 1 2 8 11 3
> > > 3 2 8 9 3
> > > 3 2 8 10 3
> > > 3 2 8 11 3
> > > 2 3 4 17 3
> > > 6 3 4 17 3
> > > 3 4 17 18 3
> > > 3 4 17 20 3
> > > 1 5 22 23 3
> > > 1 5 22 24 3
> > > 1 5 22 25 3
> > > 21 5 22 23 3
> > > 21 5 22 24 3
> > > 21 5 22 25 3
> > > 1 7 10 8 3
> > > 1 7 10 12 3
> > > 1 7 10 13 3
> > > 14 7 10 8 3
> > > 14 7 10 12 3
> > > 14 7 10 13 3
> > > 15 7 10 8 3
> > > 15 7 10 12 3
> > > 15 7 10 13 3
> > > 2 8 10 7 3
> > > 2 8 10 12 3
> > > 2 8 10 13 3
> > > 9 8 10 7 3
> > > 9 8 10 12 3
> > > 9 8 10 13 3
> > > 11 8 10 7 3
> > > 11 8 10 12 3
> > > 11 8 10 13 3
> > >
> > > ; Include Position restraint file
> > > #ifdef POSRES
> > > #include "posre.itp"
> > > #endif
> > >
> > > ; Include generic topology for ions
> > > #include "ions.itp"
> > >
> > > [ system ]
> > > ; Name
> > > %E in water
> > >
> > > [ molecules ]
> > > ; Compound #mols
> > > Protein 1
> > > SOL 2390
> > >
> > > Can somebody pelase tell what I'm doing wrong?
> > > Thanks in advance
> > > Mauro Puppett
> > >
> > > _________________________________________________________________
> > > Scarica GRATIS la versione personalizzata MSN di Internet Explorer 7!
> > > http://optimizedie7.msn.com/default.aspx?mkt=it-it_______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
Conosci Doretta? Contattala, è ora su Messenger!
http://www.doretta82.it/banner/index.html
More information about the gromacs.org_gmx-users
mailing list