[gmx-users] OPLS-AA Unknown Atomtype

[Justin A. Lemkul]

Yao Yao wrote:
> 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

The net charge problem cannot be solved by adding ions.  A fractional charge of 
that magnitude indicates the charges in the topology are wrong.

> angles, bonds, .... mentioned in the ffoplsaabon.itp, they are there.
> So I do not know any other files I may need to modify.
> 

The only file that contains [bondtypes], [angletypes], etc is ffoplsaabon.itp, 
so if the entries are indeed there, have the correct format, and are placed 
appropriately, you wouldn't be getting this error.  So unless you post the exact 
lines in their exact context, I'm left to assume that you've done something else 
wrong.

-Justin

> 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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-- 
========================================

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

========================================