no i tried with different mdin, but if i try running md using this mdin (except numexchange) it is giving the same error in the output file , Error: ifbox=2 in prmtop but angles are not correct.
Yes, i am using the different inpcrd files for different replicas as they are generated by running NVT and NPT on solvated peptide, at their respective temperature.
I am using igb=1
prmtop and inpcrd was created using xleap after adding TIP3PBOX using an octahedron box of size 9.
Carlos Simmerling <carlos.simmerling.gmail.com> wrote: and you used EXACTLY the same mdin (except numexchg)?
the same inpcrd and prmtop as well? are you using different
inpcrd for different replicas?
I'm just checking since the simulation is GB (igb=1) but
sander says that you have a prmtop with periodic box.
maybe it would help if you tell us about the box info as
far as how you built the system in leap.
On 6/18/07, priya priya <priyaanand_27.yahoo.co.in> wrote: simple MD is running but REM is not,
the error :Error: ifbox=2 in prmtop but angles are not correct,
says that the rst and prmtopp files box doen't match each other.
What should i do
REgards'
Carlos Simmerling <carlos.simmerling.gmail.com> wrote: can you run normal MD starting with the same inpcrd and prmtop?
On 6/18/07, priya priya <priyaanand_27.yahoo.co.in > wrote: Dear all
i am facing problem running rem on amber9.when i submit my job it gives an error in output file:
Error: ifbox=2 in prmtop but angles are not correct
*** input error(s)
MY input file is as follows:
am15.in - igb = 0
&cntrl
imin = 0, nstlim = 10000, dt = 0.002,
ntx = 5, temp0 = 273.0,
ntt = 1, tol = 0.000001, saltcon = 0.2,
ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
ntwx = 500, ntwe = 500, ntwr = 500, ntpr = 500,
scee = 1.2, cut = 99.0,
ntr = 0, tautp = 0.1, offset = 0.09,
nscm = 500, igb = 1, numexchg = 40000,
irest = 1, ntave = 0,
and in th error file it gives that :
[7] MPI Abort by user aborting program !
PSE: [7(5483)] Aborting program
PSE: [7]: Killing all processes, reason: Abort
forrtl: error (78): process killed (SIGTERM)
forrtl: error (78): process killed (SIGTERM)
PSIlogger: Child with rank 6 exited with status 1.
[4] MPI Abort by user aborting program !
PSE: [4(5470)] Aborting program
PSE: [4]: Killing all processes, reason: Abort
PSIlogger: Child with rank 7 exited with status 1.
PSIlogger: Child with rank 5 exited with status 1.
forrtl: error (78): process killed (SIGTERM)
PSIlogger: Child with rank 0 exited with status 1.
PSIlogger: Child with rank 4 exited with status 1.
forrtl: error (78): process killed (SIGTERM)
forrtl: error (78): process killed (SIGTERM)
PSIlogger: Child with rank 2 exited with status 1.
please help.
Regards
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Received on Wed Jun 20 2007 - 06:07:23 PDT
