Just found out what happened. Silly me. When typing the saveamberparm
command in tleap, I wrote the inpcrd file before the prmtop. So I
guess tleap was actually writing my prmtop file with an inpcrd
extension and vice-versa. Thank you for the answer and sorry for the
silly mistake.
Fabrício
2011/10/21 Jason Swails <jason.swails.gmail.com>:
> It looks like something went wrong with your topology file. It's trying to
> read an integer where it's clearly finding something else instead. If you
> send your prmtop, we may be able to take a look at it and find out what's
> happening.
>
> HTH,
> Jason
>
> 2011/10/21 Fabrício Bracht <bracht.iq.ufrj.br>
>
>> Hi, I'trying to set up a protein for molecular dynamics simulation.
>> Following advice from Amber11 manual : (igb=2 and 5) are newer, but
>> appear to give significant improvements and are recommended
>> for most projects (certainly for peptides or proteins). I decided to
>> include "set default PBradii bondi" when preparing my files using
>> tleap. The simulations worked fine before I tried this extra PBradii
>> stuff, but now sander and pmemd.cuda aren't even running. As soon as I
>> type the input line, an error comes out on screen. This is what comes
>> out for pmemd.cuda:
>> At line 301 of file prmtop_dat.f90 (unit = 8, file = 'protein.prmtop')
>> Fortran runtime error: Bad value during integer read
>> And this is what comes out for sander:
>> At line 500 of file _rdparm.f (unit = 8, file = 'protein.prmtop')
>> Fortran runtime error: Bad value during integer read
>>
>> Any help on the problem would be appreciated.
>> Thank you
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 20 2011 - 22:00:03 PDT
