[gmx-users] Acpype Parameter Error?
alanwilter at gmail.com
Mon Mar 5 16:49:20 CET 2012
Kyle, can you send and pdb file so I can reproduce your issue?
On 24 February 2012 23:25, Kyle Greenway <kgreenwa at sfu.ca> wrote:
> This email is directed mainly to Alan, who created Acpype.
> I've noticed that Acpype has assigned dihedral constants as 0.65084 for
> many dihedrals of the form X -c3-n4-X, X -c3-c3-X, and others, in my
> generated GROMACS .itp files. These dihedrals have values of 1.400 in the
> amber 99sb .dat file, which should have instead given 1.4*4.184 = 5.858 for
> the result.
> Most other dihedrals I've checked have behaved normally and their values
> correspond to what would be expected - except for dihedrals with values of
> 0.65084 in the .itp files.
> Any ideas about what's going on?
> Thanks for your time.
> Kyle Greenway
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Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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