[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,
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
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
jalemkul[at]vt.edu | (540) 231-9080
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