[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97 (Justin A. Lemkul)

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 28 00:12:20 CEST 2008

I figured out the problem.  You have nucleotides in your aminoacids.dat file, 
don't you?

For anyone who comes across this thread, have a look here:


If nucleic acid names are included in aminoacids.dat, an incorrect topology is 
produced, requiring a manual fix to the .top.  Other options are discussed at 
the above link.

I ran a test of a model DNA strand, and got integer charges for both strands. 
If I use the aminoacids.dat with nucleic acids, the charges produced are very 
badly broken.

I suggest you change your aminoacids.dat file and re-process your input, instead 
of arbitrarily adding bases on to the ends of each strand.


Ragnarok sdf wrote:
> Hello Justin. I know I just sent you an email in reply to your last one, 
> but now things seemed to have finally worked out. What I did was simply 
> to add a Cytidine residue to the 5' end and a Guanine to the 3' end of 
> each chain.
> Now all of a sudden I have integer charge and everything seems to work 
> out just fine.
> I tried this because the dickerson.pdb file test given by AMBER finishes 
> with those residues, so I thought why not try.
> Well, I am glad things worked, but still if you want me to try and 
> correct the previous errors, in order to add knowledge for future 
> gromacs' users, I would be glad to continue.
> Thank you again
> Fabrício Bracht
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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