[gmx-users] cgnr in top file

[Erik Marklund]

True. I guess gromacs groups together the terminal hydrogens, overriding 
the original force field parameters. Can't say why that decision was 
made, but it will influence your simulation very little.

Erik

leila karami skrev:
> Dear Erik
>  
> you said Amber03 was not parameterized with charge groups and last 
> column in your rtp entry holds the chargegroup numbers. but
> cgnr column in my top file does not looks just like it. in case of H1, 
> H2 and H3.
>  
> /     H1    amber99_17   0.16420     2
> //     H2    amber99_17   0.16420     3
> //     H3    amber99_17   0.16420     4
> //    // /. that's ok. but why
>  
> /and my top file is as follow :
> //  
> //                                                        
> //    nr       type          resnr  residue  atom   cgnr   charge     
> mass  
> //      //2 amber99_17      1   NGLY     H1      2     0.1642      1.008  
> //      3 amber99_17      1   NGLY     H2      2     0.1642      1.008  
> //      4 amber99_17      1   NGLY     H3      2     0.1642      1.008   
> //   /
> thanks for your attention        


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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
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erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/