AMBER Archive (2009)

Subject: [AMBER] The problem of restart file

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Wed Jul 01 2009 - 07:15:34 CDT

Dear AMBER users,

    I performed a long md simulation by repeating restarts. But at the 28th segment, the simulation can't be continued because the pmemd can't open the restart file (npt28.rst). Here are some error message:
in .out file: 

---
....
&cntrl                                                                         
   imin=0,                                                                     
   ntx=5, irest=1,                                                             
   ntpr=100, ntwx=1000,ntwr=5000,                                              
   dt=0.002,nstlim=1000000, nscm=1000,                                         
   cut=9.,dielc=1.0,                                                           
   ntc=2, ntf=2,                                                               
   ntb=2,                                                                      
   ntp=1,pres0=1.0,taup=3.0,                                                   
   ntt=1, tautp=3.0,temp0=300.0,                                               
   ioutfm=1                                                                    
/                           
| ERROR:   Could not read coords from npt28.rst   
---------------

When using ambpdb to convert from npt28.rst to npt28.pdb using the command: ambpdb -p mono10.prmtop < npt28.rst > npt28.pdb

 errors are: 
------------
| New format PARM file being parsed.
| Version =    1.000 Date = 05/19/09 Time = 22:55:51
forrtl: severe (64): input conversion error, unit 5, file stdin
Image              PC                Routine            Line        Source             
ambpdb             00000000004A593E  Unknown               Unknown  Unknown
ambpdb             00000000004A4B3E  Unknown               Unknown  Unknown
ambpdb             000000000045498A  Unknown               Unknown  Unknown
ambpdb             000000000041E172  Unknown               Unknown  Unknown
ambpdb             000000000041D9A1  Unknown               Unknown  Unknown
ambpdb             0000000000439716  Unknown               Unknown  Unknown
ambpdb             000000000040D194  Unknown               Unknown  Unknown
ambpdb             00000000004058FD  Unknown               Unknown  Unknown
ambpdb             00000000004034CC  Unknown               Unknown  Unknown
libc.so.6          0000003083C1D8A4  Unknown               Unknown  Unknown
ambpdb             00000000004033D9  Unknown               Unknown  Unknown       
-----------        

Does anyone encounter the similar problems? 
Any suggestion is greatly appreciated.

Thanks.

Jeffry              

-----------
Dalian Institute of Chemical Physics,
Chinese Academy of Sciences
Dalian, China
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