Hi,
This should now be fixed in the GitHub version:
https://github.com/Amber-MD/cpptraj/pull/929
Give it a try and let me know if it works for you. If so, I can work
on making it a patch for the AmberTools version.
Thanks,
-Dan
On Sun, Jan 9, 2022 at 5:13 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Sorry, this kind of fell off my radar. I did reproduce the issue and I
> should be able to get a fix in for it tomorrow (I hope, barring any
> more delays...).
>
> Thanks again for the report.
>
> -Dan
>
> On Sun, Jan 9, 2022 at 11:43 AM Chris Lee
> <chrishankyu.lee.mail.utoronto.ca> wrote:
> >
> > Hi Dan,
> >
> > I have the same issue with AmberTools21 (cpptraj V.5.1.0). I haven't been able to successfully compile the GitHub version of cpptraj on my local machine so I can't say anything about that.
> > However, on my local machine I also get a number 11 at the end of the segmentation fault error line like so: "Segmentation Fault: 11", if that means anything.
> >
> > Do you have any other suggestions?
> >
> > Thanks,
> > Chris
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Monday, December 20, 2021 4:52 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file
> >
> > [You don't often get email from daniel.r.roe.gmail.com. Learn why this is important at http://aka.ms/LearnAboutSenderIdentification.]
> >
> > Hi,
> >
> > I recommend upgrading to amber tools 21 or the GitHub version of cpptraj:
> > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FAmber-MD%2Fcpptraj&data=04%7C01%7Cchrishankyu.lee%40mail.utoronto.ca%7C4a1902b97a58408927e008d9c4031059%7C78aac2262f034b4d9037b46d56c55210%7C0%7C0%7C637756340121975828%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=wy%2B%2BFJsLEmkEq62z%2Fy2S8M6ErvCelUjTze17A7ba2E0%3D&reserved=0
> >
> > See if that helps,
> >
> > -Dan
> >
> > On Mon, Dec 20, 2021 at 4:40 PM Chris Lee <chrishankyu.lee.mail.utoronto.ca>
> > wrote:
> >
> > > Hi Dan,
> > >
> > > I don't know if CPPTRAJ has its own version releases separate from amber,
> > > but I am using amber18.
> > >
> > > Thanks,
> > > Chris
> > > ________________________________
> > > From: Daniel Roe <daniel.r.roe.gmail.com>
> > > Sent: Monday, December 20, 2021 2:06 PM
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Subject: Re: [AMBER] CPPTRAJ Segmentation Fault with modified topology file
> > >
> > > [You don't often get email from daniel.r.roe.gmail.com. Learn why this is
> > > important at http://aka.ms/LearnAboutSenderIdentification.]
> > >
> > > Hi,
> > >
> > > Which version of cpptraj?
> > >
> > > -Dan
> > >
> > > On Mon, Dec 20, 2021 at 1:58 PM Chris Lee <
> > > chrishankyu.lee.mail.utoronto.ca>
> > > wrote:
> > >
> > > > Hi All,
> > > >
> > > > I've recently used the ff14IDP force field (code found here:
> > > >
> > > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchaohao2010%2FADD-CMAP&data=04%7C01%7Cchrishankyu.lee%40mail.utoronto.ca%7C4a1902b97a58408927e008d9c4031059%7C78aac2262f034b4d9037b46d56c55210%7C0%7C0%7C637756340121975828%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=7r%2FhRS2%2BZ6hOwEVASppPbKyS2OaLIwYt3SUuMvaTbkg%3D&reserved=0)
> > > to run some MD. The actual
> > > > simulation was completed successfully without any issues; however, when I
> > > > try to analyze the trajectory using CPPTRAJ, I get a Segmentation Fault
> > > > error message after trying to load the topology file via the "parm"
> > > command
> > > > and CPPTRAJ exits without any further details. I can send the topology
> > > file
> > > > in question if requested. Any help would be appreciated.
> > > >
> > > > Thanks,
> > > > Chris
> > > > _______________________________________________
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Received on Mon Jan 10 2022 - 08:00:02 PST
