Your restart (the one you first posted) had the same issue - no EOL. I
fixed it the same way. You should really figure out what went wrong
generating these files.
-Dan
On Mon, Jun 22, 2020 at 2:37 PM Jag Silwal <jagsilwal.gmail.com> wrote:
>
> Dan,
>
> Thank you for the file. This time, I tried both ways using the corrected
> file you sent me. Now I am getting error messages as follows:
>
>
> *ambpdb -p act2.top <act2.crd> h++.pdb*
>
> *Error: Unable to read restart atoms/time.*
>
> AND
> ambpdb -p act2.top -c act2.crd > h++.pdb
>
>
> *Error: Could not determine trajectory act2.crd format.*
>
> I have attached the .crd file here (attaching both files bounced my email
> as it is too big) here, just in case you would be able to look at both
> files and give me some suggestions. I am stuck at this point and I am not
> being able to move this project forward. I greatly appreciate your help.
>
>
> Thanks again
>
>
> On Fri, Jun 19, 2020 at 10:05 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Fri, Jun 19, 2020 at 5:56 PM Jag Silwal <jagsilwal.gmail.com> wrote:
> > > could you please send me the file with the EOL,
> > > as an example, so that I can proceed with the ambpdb?
> >
> > Sure, attached. FYI, it's as simple as 1) open up the file in a text
> > editor, 2) Add a blank line to the end of the file, 3) remove that
> > blank line. That should ensure an EOL is written. Let me know if it
> > still doesn't work for some reason.
> >
> > -Dan
> >
> > >
> > >
> > > On Fri, Jun 19, 2020 at 5:30 PM Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > >
> > > > Hi,
> > > >
> > > > The actual problem here is the topology file has no EOL; cpptraj
> > > > attempts to read the IPOL section and gets fewer bytes than expected,
> > > > and so returns the error. I opened the file in a text editor, added
> > > > the EOL and voila, it works.
> > > >
> > > > On Fri, Jun 19, 2020 at 4:41 PM David A Case <david.case.rutgers.edu>
> > > > wrote:
> > > > >
> > > > > As the message says, your prmtop file has an FLAG IPOL section (at
> > the
> > > > > very end). This is not a known flag, and cpptraj/ambpdb gives the
> > above
> > > >
> > > > This is actually a known flag, although I think it may be deprecated.
> > > > Cpptraj will read it as long as there are no other problems with the
> > > > file.
> > > >
> > > > > You need to figure out how the prmtop file was created in the first
> > > > > place: if it was from the H++ server, you might try contacting them
> > to
> > > > > see if they can help.
> > > >
> > > > I second this. If they are writing files with no EOL that's probably
> > > > not the intended behavior.
> > > >
> > > > > (for Dan: sometimes, cpptraj will just complain but soldier on if it
> > > > > finds unknown FLAGs; sometimes it seems to stop; sometimes it seems
> > to
> > > >
> > > > It should always be fine as long as the FLAGs it expects are there
> > > > (like atom names, residue indices, etc). Unknown flags should be fine.
> > > > If you have an example where this is not the case please let me know
> > > > (and/or open up an issue on GitHub!).
> > > >
> > > > -Dan
> > > >
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Received on Wed Jun 24 2020 - 06:00:06 PDT
