[gmx-users] Re: Alcohol Dehydrogenase MD simulation....Reg

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 26 18:53:31 CET 2011

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Kishore wrote:
> Dear Mark,
> As you correctly pointed out, I had looked into those improper dihedral 
> specifications several times before and it seems that they are properly 
> mentioned in the .itp file. I have been using the topologies generated 
> by PRODRG server for NADPH as i could not make it comply with the 
> inbuilt residue template library topologies. In this topologies 
> generated by PRODRG there is a directive called [ dihedrals ] and it 
> listed out all the dihedrals with comment lines showing proper and 
> improper dihedrals, but this seems to differ from the way the the 
> topologies are defined in the gromacs inbuilt template library which 
> only lists out the impropers. Does this make any difference in terms of 
> grompp interpreting them during the preprocessing? I am herein pasting a 
> section of that dihedrals and a snapshot of the NADPH molecule with the 
> atom names labelled so that you can see that the impropers you mentioned 
> in your reply are infact mentioned in the .itp file I am using.

Gromacs separates proper and improper dihedrals in [dihedrals] directives, 
presumably for convenience.  Having one or two directives with proper contents 
does not make a difference.  If, however, PRODRG is assigning parameters that 
the force field library does not, that just sounds like typical PRODRG behavior 
- its parameters are often incorrect and one has to know the proper way to 
handle re-assigning parameters.  Bonded parameters are often more correct than 
charges and charge groups from PRODRG, which are wrong in all the cases I've 
ever seen.



> The three improper dihedrals you have mentioned are highlighted 
> below...please correct me in case if i am getting the meaning 
> wrong..Sorry for flooding with long posts, but I am in a great need for 
> some help on this.
> [ dihedrals ]
> ; ai  aj  ak  al  fu    c0, c1, m, ...
>    1   4   3   2   2      0.0  167.4        0.0  167.4   ; imp   NBS  
> CBQ  H8M  HBS  
>    4   1   5   6   2      0.0  167.4        0.0  167.4   ; imp   CBQ  
>    6   4   9   7   2      0.0  167.4        0.0  167.4   ; imp   CAV  


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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