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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- application/octet-stream attachment: act2.crd
Received on Mon Jun 22 2020 - 12:00:03 PDT
