H-bond analysis in case of TIP4P water model ?
Hello, it seem to me that Chimera is not able to do H-bond analysis between water molecules when TIP4P water model is used. Am I right or I overlooked something ? Thank you very much for the answer in advance ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
On Sep 3, 2012, at 6:28 AM, Marek Maly wrote:
Hello,
it seem to me that Chimera is not able to do H-bond analysis between water molecules when TIP4P water model is used. Am I right or I overlooked something ?
Hi Marek, I am not aware of any such problem. Could you use Help->Report A Bug to send in a bug report, and provide more details about the problem you are having (what structure you used, what you did, what happened)? Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Sep 3, 2012, at 6:28 AM, Marek Maly wrote:
Hello,
it seem to me that Chimera is not able to do H-bond analysis between water molecules when TIP4P water model is used. Am I right or I overlooked something ?
Upon further review, I can reproduce the problem you're having. The "extra point" of the TIP4P water (atom "EPW") is screwing up Chimera's H-bond finding. You need to delete that "atom" ("del @epw" in the command line), then Chimera will be able to find the inter-water H bonds. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (2)
-
Eric Pettersen -
Marek Maly