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://1drv.ms/u/s!AuyAusivBfCSiA3u1cQ9FZHpZrAl
https://1drv.ms/u/s!AuyAusivBfCSiAiKNyix-6pS0fiC<
https://1drv.ms/u/s%21AuyAusivBfCSiAiKNyix-6pS0fiC>
Any help would be greatly appreciated.
Thanks in Advance
Ramin Salimi
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Received on Fri Mar 31 2017 - 14:30:02 PDT
