On 2012-11-19 10:42, Albert wrote:
On 11/19/2012 10:27 AM, David van der Spoel wrote:
On 2012-11-19 09:57, Albert wrote:
hello:
I've got a K+ near an Asp residue. I found that If I include the K+
in H++ calculation, the Asp is deprotonated while it is protonated if I
didn't include it. I am quite confused for this. I am just wondering
will the g_protonate will solve this problem?
thank you very much.
best
Albert
This makes sense! The environment is made for a neutral group, which
you get by either having a K+ or a proton near the Asp.
Normal pdb2gmx will give you the correct topology.
hello David:
thanks a lot for such kind reply and comments.
Is there any paper concerning on this ion issue? The pdb2gmx make
correct protonation state of residues in most case, however for some
special case we probably need more solid evidence to be confirmed. Since
the protonation state of residue have great impact on later MD productions.
No paper, just basic biochemistry.
In case you suspect an amino-acid should NOT have the default
protonation you can run pdb2gmx interactively. This is however your
responsibility as the algorithm is not perfect, in fact it only checks
the protonation of histidine residues.
thank you very much.
best
Albert
--
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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