Can you post exact error here?
cheers
Hai
On Fri, Mar 31, 2017 at 5:30 PM, Ramin Salimi <ramin.salimi01.utrgv.edu>
wrote:
> Hai
>
> That is right. I made that mistake but then corrected that but received
> similar errors of the same nature such that just the number of lines in the
> error changed.
>
>
> Ramin
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Friday, March 31, 2017 4:27:14 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Issues Regaring the PDB files from Trajectory frames
>
> > At line 297 of file prmtop_dat.F90(unit=8, file= out_frame.pdb.4840)
>
> You're supposed to pass prmtop file, not pdb file (out_frame.pdb)?
>
> Hai
>
> On Fri, Mar 31, 2017 at 5:23 PM, Ramin Salimi <ramin.salimi01.utrgv.edu>
> wrote:
>
> > Dear Amber users
> >
> > I have picked some frames at different elongations from my trajectory
> file
> > to make PDB files. The following is my script to be used in cpptraj:
> >
> > parm revnelson.smd.prmtop
> > trajin smd.mdcrd
> > strip :WAT,Na+
> > center :1-24 mass origin
> > image origin center familiar
> > trajout out_frame.pdb pdb multi nobox onlyframes
> > 1412,1630,2790,3700,3933,4840,4958,5443,7278
> > Then, I solvate and neutralize them, and make topology and coordinate
> > files for each of the newly created pdb files. However, in the first
> > minimization step, I get the following:
> > At line 297 of file prmtop_dat.F90(unit=8, file= out_frame.pdb.4840)
> > Fortran runtime error= bad value during integer read OR
> > At line 71 of file rdparm.F90(unit=8, file= out_frame.pdb.4840)
> > Fortran runtime error= bad value during integer read OR
> >
> > At line 551 of file mdin_ctrl_dat.F90(unit=5, file=min1.in)
> >
> > Fortran runtime error= end of file
> > OR
> >
> > At line 587 of file mdread.F90((unit=5, file=min1.in)
> >
> > Fortran runtime error= end of file
> >
> > or similar errors.
> >
> > I think there is something wrong with my parameter and/or coordinate
> > file(s) created from the frame, but I do not know how to fix it.
> >
> > I have attached pdb file, the parameter and coordinate files from that
> pdb
> > file, AND ALSO, parameter(revnelson.smd.prmtop) and trajectory files
> from
> > which I extracted pdb files. The links to the attachments are provided
> > below:
> >
> > https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2F1drv.ms%2Fu%2Fs!AuyAusivBfCSiA3u1cQ9FZHpZrAl&
> data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C32d3b81590c1427fe0d408d4787c
> b8ae%7C990436a687df491c91249afa91f88827%7C0%7C0%
> 7C636265924449752371&sdata=fBS5SAH8S0UielZ3wEkMYq%
> 2BTZEhZHmRiVdQZc4uBUpI%3D&reserved=0
> >
> > https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2F1drv.ms%2Fu%2Fs!AuyAusivBfCSiAiKNyix-6pS0fiC&
> data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C32d3b81590c1427fe0d408d4787c
> b8ae%7C990436a687df491c91249afa91f88827%7C0%7C0%
> 7C636265924449752371&sdata=fhWBlkMOv9yNPAgImOOPGtd0jNOg0u
> hihjBkKd93Tio%3D&reserved=0<https://na01.safelinks.
> protection.outlook.com/?url=https%3A%2F%2F1drv.ms%2Fu%2Fs%
> 25&data=02%7C01%7Cramin.salimi01%40utrgv.edu%
> 7C32d3b81590c1427fe0d408d4787cb8ae%7C990436a687df491c91249afa91f8
> 8827%7C0%7C0%7C636265924449752371&sdata=5UQBiPJQpFwc5uUKj3u1ek9%
> 2FHUEQU7ik9ED%2Ften0GqM%3D&reserved=0
> > 21AuyAusivBfCSiAiKNyix-6pS0fiC>
> >
> > Any help would be greatly appreciated.
> >
> > Thanks in Advance
> >
> > Ramin Salimi
> > _______________________________________________
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> 8827%7C0%7C0%7C636265924449752371&sdata=UjyWsWYNY6k3B6X%
> 2BcdwTtRGvys87YjjNyjV74Y0EhKo%3D&reserved=0
> >
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Received on Fri Mar 31 2017 - 15:00:03 PDT
