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-- Jason Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 On Jul 21, 2010, at 9:37 AM, nicholus bhattacharjee <nicholusbhattacharjee.gmail.com> wrote: > Dear Jason, > Thank you for your kind help. I have some other problems > also. As you can see from my earlier I am running 10 nano seconds constant > pH simulation in two batches of 5 nano seconds each. Now when the 5 nano > second run is over I am able to generate the properties (like rmsd, trajout) > from the trajectory file. But both my output files csprestrt and prod.rts > files are corrupted for example > > if I do > > $ ambpdb -p prmtop <prod.rst> x.pdb > > its giving error msg > > | New format PARM file being parsed. > | Version = 1.000 Date = 07/06/10 Time = 17:54:02 > At line 624 of file _ambpdb.f (unit = 5, file = 'stdin') > Fortran runtime error: Bad value during floating point read > > I am unable to understand what is the problem. My prod.out file is giving > the analysis of the whole trajectory. Please help... > > On Mon, Jul 12, 2010 at 10:04 AM, Jason Swails <jason.swails.gmail.com>wrote: > >> Hello, >> >> The cprestrt looks quite strange... However, this step described in the >> manual is only necessary if you feel the need to get rid of all the >> extraneous zeroes that crop up because you're not titrating the maximum >> number of residues (50). sander simply dumps the contents of the whole >> &cnstph namelist to the cprestrt file, then reads the contents of the >> &cnstph namelist when it reads the cpin file. Therefore, you can just use >> the cprestrt as the cpin file directly without any modification. >> >> Good luck! >> Jason >> >> On Mon, Jul 12, 2010 at 12:23 AM, nicholus bhattacharjee < >> nicholusbhattacharjee.gmail.com> wrote: >> >>> Dear community, >>> I am running a constant pH MD of 10 nano seconds >> in >>> a remote cluster. Since there is a cut of time of 72 hrs for user I have >> to >>> break the simulation into two parts of 5 ns each. Now after the first 5 >> ns >>> simulation is over I have go cprestrt file from the simulation. According >>> to >>> the manual I have to conver this cprestrt file to cpin2 file with the >>> following command >>> >>> $ cpintil.pl cprestrt > cpin2 >>> >>> >>> But it is showing the following errors >>> >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in numeric lt (<) at >>> /usr/local/amber9/exe/CPin.pm line 238. >>> Use of uninitialized value in array dereference at >>> /usr/local/amber9/exe/CPin.pm line 186. >>> Can't call method "AtomCount" on an undefined value at >>> /usr/local/amber9/exe/CPin.pm line 61. >>> >>> >>> I am unable to understand what to do. Please help. I am attaching the >>> cprestrt file. >>> >>> -- >>> Nicholus Bhattacharjee >>> PhD Scholar >>> Department of Chemistry >>> University of Delhi >>> Delhi-110007 (INDIA) >>> Phone: 9873098743(M) >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >>> >> >> >> -- >> Jason M. Swails >> Quantum Theory Project, >> University of Florida >> Ph.D. Graduate Student >> 352-392-4032 >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > Nicholus Bhattacharjee > PhD Scholar > Department of Chemistry > University of Delhi > Delhi-110007 (INDIA) > Phone: 9873098743(M) > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jul 21 2010 - 11:30:04 PDT