On 2011-03-31 17.19, Alan Wilter Sousa da Silva wrote:
I know it's supported.
I was just investigating the possibility since I build acpype to create
topologies for gromacs, but also it converts from amber to gromacs (like
amb2gmx.pl <http://amb2gmx.pl>), and so I was wondering about RB with 6
coefficients since multiple proper dihedrals is only supported for gmx
4.5 and above.
Unfortunately RB only goes to 5 and it would be a pain to support more
since the tpr format would have to be updated. The current solution with
the type 9 dihedrals is a royal pain in the neck too. I've actually
written a script that converts the present rtp files to contain *all*
bonded interactions explicitly (with parameters), and it replaces the 9
type dihedrals with multiple 1 type dihedrals (lots of them with all
zeros, LOL).
But I don't want to fuss about it. If to forget about GMX 4.0.x and
below is the way, so it will be.
Thanks,
Alan
On 31 March 2011 16:08, David van der Spoel <sp...@xray.bmc.uu.se
<mailto:sp...@xray.bmc.uu.se>> wrote:
On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote:
Hi there,
Since ILDN dihedrals has some parameters with up to periodicity
6, I was
wondering if it's possible to convert it in RB with 6
coefficients. If
so, what would be the formula? For example, for converting the usual
Amber99SB to RB I have:
ILDN is already supported in the latest gromacs releases, by simply
using multiple proper dihedrals. Why would you want to change it?
if phase in [0, 180]:
if kPhi > 0: V[period] = 2 * kPhi * cal
if period == 1:
C[0] += 0.5 * V[period]
if phase == 0:
C[1] -= 0.5 * V[period]
else:
C[1] += 0.5 * V[period]
elif period == 2:
if phase == 180:
C[0] += V[period]
C[2] -= V[period]
else:
C[2] += V[period]
elif period == 3:
C[0] += 0.5 * V[period]
if phase == 0:
C[1] += 1.5 * V[period]
C[3] -= 2 * V[period]
else:
C[1] -= 1.5 * V[period]
C[3] += 2 * V[period]
elif period == 4:
if phase == 180:
C[2] += 4 * V[period]
C[4] -= 4 * V[period]
else:
C[0] += V[period]
C[2] -= 4 * V[period]
C[4] += 4 * V[period]
So, as you can see, I can handle up to 4 periods (C[5] is always
0, but
not with ILDN and I need to add C[6] rules as well).
Any ideas? Many thanks in advance,
Alan
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
http://folding.bmc.uu.se
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--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
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