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 - 08:00:01 PDT
