[gmx-users] missing parameters in auto-generated topology file?

[Justin A. Lemkul]

Yun Shi wrote:
> Hi all,
> 
> I used pdb2gmx and selected amber99sb for generation of itp files of a 
> normal peptide within GROMACS 4.5.4.
> 
> But I saw that all the bonds, angles, and dihedral parameters (c0, c1, 
> c2 ...) were not present in the itp file, while only funct is defined. 
> It seems the same thing happens with opls ff.
> 
> So I wonder if those parameters are automatically generated according to 
> corresponding atom types when implementing grompp? What would happen if 

Yes, they're read from ffnonbonded.itp.

> I have exotic species and some atomic sequences are not defined in the   
> [ angletypes ] or   [ dihedraltypes ] section of amber99sb.ff/ffboned.itp ?
> 

You'd get a fatal error that there are no default bonded types for those 
interactions.

> 
> In the other case, when I used amb2gmx.pl <http://amb2gmx.pl> to convert 
> glycam force field-parametized prmtop file to gromacs top file, I saw 
> something like:
> 
> [ dihedrals ]
> ;i  j   k  l     func   C0  ...  C5
>     19   18   20   21     3     0.75312     2.25936     0.00000    
> -3.01248     0.00000     0.00000     ;
>     41   1    18   19     3     0.20920     0.62760     0.00000    
> -0.83680     0.00000     0.00000     ;
> 
> 
> 
> Although I understand '3' in the fifth column indicates a 
> Ryckaert-Bellemans-potential function, but what parameters are those 
> numbers followed (0.75312     2.25936     0.00000    -3.01248     
> 0.00000     0.00000) correspond to?
> 

Please see manual section 4.2.12 and the table therein pertaining to 
Ryckaert-Bellemans dihedral coefficients.

-Justin

> Thanks for any help!
> 
> Yun
> 

-- 
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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

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