Hi Dan,
I just read your message about implementing AQUA-DUCT into cpptraj.
I'd loved to, that would be a very interesting challenge!
Please contact my supervisor, who is responsible also for the software
development process: a.gora.tunnelinggroup.pl
Best regards,
Karolina
śr., 14 kwi 2021 o 16:48 Daniel Roe <daniel.r.roe.gmail.com> napisał(a):
> Hi,
>
> First, you could combine the two hbond commands (unless you actually
> want them separated) by omitting 'donormask' and just specifying
> residue 1639:
>
> hbond dist 4.0 :1639 HB-Oxygen angle -1 out hbondAacc.dat avgout
> ocygen_avg.dat solventacceptor :OXY solventdonor :OXY
>
> Second, segfaults can result from bugs, but they can also be from
> memory issues etc - it's hard to tell without more information. What
> version of cpptraj are you using? Does it happen if you only process a
> few trajectory frames (use e.g. 'trajin <mytraj> 1 10'). Can you send
> me off-list the full output from cpptraj if possible? Thanks
>
> -Dan
>
> On Wed, Apr 14, 2021 at 10:16 AM Damiano Spadoni
> <Damiano.Spadoni.nottingham.ac.uk> wrote:
> >
> > Dan,
> >
> > I made an attempt to run the hbond command that you suggested on your
> last email but I am only facing "segmentation fault" issues.
> > If I want to investigate how many OXY residues (resname for molecular
> oxygen) get into the active site at a distance <= 4 Angstrom from the
> FeS-cluster (resid 1639) I will type the following command:
> >
> > hbond dist 4.0 donormask :1639 HB-Oxygen angle -1 out hbondAacc.dat
> avgout ocygen_avg.dat solventacceptor :OXY solventdonor :OXY
> >
> > hbond dist 4.0 acceptormask :1639 out hbondBacc.dat avgout
> hbondAVG_Aacc.dat
> >
> > Both commands only give segmentation fault issues.
> > Is there something I forgot to look at?
> >
> > Kind regards,
> > Damiano
> >
> > ________________________________
> > From: Damiano Spadoni <Damiano.Spadoni.nottingham.ac.uk>
> > Sent: Tuesday, April 13, 2021 3:17 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] How to track oxygen molecules in MD
> >
> > Thank you both for suggestions.
> > I downloaded AQUADUCT and I was going to give it a try as it seems to be
> a straightforward calculation.
> > I'll compare it with the new hbond command Dan just provided.
> > Speaking of new implementations, AQUADUCT could be useful in cpptraj as
> well as a protein tunnel calculation software (e.g. CAVER) to increase
> structural investigations in proteins.
> >
> > Damiano
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Tuesday, April 13, 2021 2:48 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] How to track oxygen molecules in MD
> >
> > Hi,
> >
> > On Mon, Apr 12, 2021 at 12:51 PM Damiano Spadoni
> > <Damiano.Spadoni.nottingham.ac.uk> wrote:
> > > The same simulation contains O2 molecules within the water solvent. I
> am interested in looking at the number of O2 molecules that enter the
> active site and approach the metal cluster over the simulation and track
> the route of the identified O2 molecule(s).I looked at the possibilities to
> retrieve so by using cpptraj by I failed with the hbond command (because
> there is no h-bonding between O2 and [4Fe-4S] cluster) as well as looking
> at native contacts or using the closest command.
> >
> > You don't actually need hydrogen bonds to form; you can just make it
> > so that there is no angle criterion (by specifying 'angle -1'), only a
> > distance criterion. You can also make tracking the oxygen non-specific
> > by using the solventdonor/solventacceptor keywords and treating them
> > as "solvent", e.g. 'hbond HB-Oxygen angle -1 out nhb.agr avgout
> > oxygen_avg.dat solventacceptor <oxygen mask> solventdonor <oxygen
> > mask>'.
> >
> > However, the code recommended by Karolina may be closer to what you
> > need. @Karolina any chance you want to implement AQUA-DUCT in cpptraj?
> > :-)
> >
> > -Dan
> >
> > > I failed with the implicit ligand sampling tool in VMD too and I want
> to ask you if you know of any other turnaround to calculate that.
> > >
> > > Kind regards,
> > > Damiano Spadoni
> > >
> > >
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Received on Wed Apr 14 2021 - 08:30:03 PDT
