I think I have identified where the problem lies. We are using mixed forcefields to describe an amino acid based surfactant (the hydrophobic tail identified by the GAFF forcefield and amino acid polar head groups identified by the protein forcefield). When we ran antechamber on the surfactant and only used the GAFF forcefield to describe the entire surfactant molecule we did not observe the problem. So Now I just need to identify what I did wrong in using the mixed forcefields to describe the amino acid based surfactant.
-----Original Message-----
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, June 9, 2020 3:38 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Xleap - disappearance of selection when trying to relax selection
On Tue, Jun 09, 2020, Billiot, Eugene wrote:
>I am having a problem in Xleap when I build a unit, select that unit
>and then try to relax it in Xleap. More often than not, at least
>lately, instead of showing the unit relaxing it simply disappears.
>What we have been doing is just repeat the whole process of building
>the unit and trying to relax it until it finally relaxes. We repeat
>the exact steps each time so it is not how we build the unit. Any
>ideas what is going on and how we resolve the issue.
I don't see this behavior on my machine. Can you say what OS and compiler you are using? Maybe also a summary of what you did: are you editing an existing unit, or creating one entirely from scratch?
That said, graphically building molecules in xleap is surely on its last legs. I don't think anyone know much about how to fix the problem anymore. I personally tend to use Avogadro for such tasks, but I've never made any attempt to compare different programs.
There *is* an Amber-aware tleap/xleap replacement in the works, but it is not really ready yet.
....regards...dac
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Received on Wed Jun 10 2020 - 07:00:02 PDT
