[gmx-users] OPLS-AA Unknown Atomtype

[Yao Yao]

HI Justin,

I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions.

So I do not think ions addition will help. And I double-checked the angles, bonds, .... mentioned in the ffoplsaabon.itp, they are there.
So I do not know any other files I may need to modify.

Thanks,

yao




________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, August 29, 2011 3:41 AM
Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype



Yao Yao wrote:
> Hi Justin,
> 
> Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp,
> but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like,
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> checking input for internal consistency...
> processing topology...
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
> Generated 338253 of the 338253 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 338253 of the 338253 1-4 parameter combinations
> 
> ERROR 1 [file cro.top, line 37]:
>   No default Bond types
> 
> 
> ERROR 2 [file cro.top, line 71]:
>   No default Angle types
> 
> 
> ERROR 3 [file cro.top, line 72]:
>   No default Angle types
> 
> 
> ERROR 4 [file cro.top, line 85]:
>   No default Angle types
> 
> 
> ERROR 5 [file cro.top, line 91]:
>   No default Ryckaert-Bell. types
> 
> 
> ERROR 6 [file cro.top, line 92]:
>   No default Ryckaert-Bell. types
> 
> 
> ERROR 7 [file cro.top, line 93]:
>   No default Ryckaert-Bell. types
> 
> 
> ERROR 8 [file cro.top, line 108]:
>   No default Ryckaert-Bell. types
> 
> 
> ERROR 9 [file cro.top, line 112]:
>   No default Proper Dih. types
> 
> 
> ERROR 10 [file cro.top, line 113]:
>   No default Proper Dih. types
> 
> 
> ERROR 11 [file cro.top, line 114]:
>   No default Proper Dih. types
> 
> Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 2 bonded neighbours molecule type 'SOL'
> 
> NOTE 1 [file cro.top, line 142]:
>   System has non-zero total charge: -1.022478e+00
>  

This total charge suggests that your topology is badly broken.

> 
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> 
> There was 1 note
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: grompp.c, line: 986
> 
> Fatal error:
> There were 11 errors in input file(s)
> -----------------------------------------------
> 
> I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values?
> 

If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors.  Double check again.

-Justin

-- ========================================

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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