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%7C32d3b81590c1427fe0d408d4787cb8ae%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%7C32d3b81590c1427fe0d408d4787cb8ae%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636265924449752371&sdata=fhWBlkMOv9yNPAgImOOPGtd0jNOg0uhihjBkKd93Tio%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%7C990436a687df491c91249afa91f88827%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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Received on Fri Mar 31 2017 - 15:00:02 PDT
