>
> Dear Mark,
Thanks very much for your advise, I followed it and remove the cruft in
these two files. I think it works well, but there is another problem
coming. When I read the hem_ryd.in, the commands are as follows:
> loadamberprep hem_ryd.in
Loading Prep file: ./hem_ryd.in
253 pairs of atoms within potential bonding distance
206 are not H-H pairs
Atom .R<1 1>.A<C1C 38> has maximum number of bonds.
Atom .R<1 1>.A<C1D 54> has maximum number of bonds.
Atom .R<1 1>.A<HA 64> has maximum number of bonds.
Atom .R<1 1>.A<CBD 68> has maximum number of bonds.
Atom .R<1 1>.A<C1B 22> has maximum number of bonds.
Atom .R<1 1>.A<CBC 48> has maximum number of bonds.
Atom .R<1 1>.A<CBB 32> has maximum number of bonds.
Atom .R<1 1>.A<HBC1 49> has maximum number of bonds.
Atom .R<1 1>.A<HBB2 34> has maximum number of bonds.
Atom .R<1 1>.A<HBC2 50> has maximum number of bonds.
Atom .R<1 1>.A<HBB1 33> has maximum number of bonds.
Atom .R<1 1>.A<HB 21> has maximum number of bonds.
Atom .R<1 1>.A<HD 53> has maximum number of bonds.
Atom .R<1 1>.A<HA 64> has maximum number of bonds.
Atom .R<1 1>.A<HC 37> has maximum number of bonds.
Atom .R<1 1>.A<CHC 36> has maximum number of bonds.
Atom .R<1 1>.A<CHD 52> has maximum number of bonds.
Atom .R<1 1>.A<HMA3 18> has maximum number of bonds.
Atom .R<1 1>.A<HMC1 42> has maximum number of bonds.
Atom .R<1 1>.A<HAA2 7> has maximum number of bonds.
Atom .R<1 1>.A<HMD3 60> has maximum number of bonds.
Atom .R<1 1>.A<HAD2 67> has maximum number of bonds.
Atom .R<1 1>.A<HMB3 28> has maximum number of bonds.
Atom .R<1 1>.A<HMA2 17> has maximum number of bonds.
Atom .R<1 1>.A<HMD2 59> has maximum number of bonds.
Atom .R<1 1>.A<HMB2 27> has maximum number of bonds.
Atom .R<1 1>.A<HMC2 43> has maximum number of bonds.
Atom .R<1 1>.A<HMB1 26> has maximum number of bonds.
Atom .R<1 1>.A<HAD1 66> has maximum number of bonds.
Atom .R<1 1>.A<HMD1 58> has maximum number of bonds.
Atom .R<1 1>.A<HAA1 6> has maximum number of bonds.
Atom .R<1 1>.A<HMC3 44> has maximum number of bonds.
Atom .R<1 1>.A<HMA1 16> has maximum number of bonds.
Atom .R<1 1>.A<CGA 11> has maximum number of bonds.
Atom .R<1 1>.A<CGA 11> has maximum number of bonds.
Atom .R<1 1>.A<CBA 8> has maximum number of bonds.
Atom .R<1 1>.A<CBA 8> has maximum number of bonds.
Atom .R<1 1>.A<CBD 68> has maximum number of bonds.
Atom .R<1 1>.A<CBD 68> has maximum number of bonds.
Atom .R<1 1>.A<CGD 71> has maximum number of bonds.
Atom .R<1 1>.A<CGD 71> has maximum number of bonds.
Atom .R<1 1>.A<HBA2 10> has maximum number of bonds.
Atom .R<1 1>.A<HBD2 70> has maximum number of bonds.
Atom .R<1 1>.A<HBD1 69> has maximum number of bonds.
Atom .R<1 1>.A<HBA1 9> has maximum number of bonds.
Atom .R<1 1>.A<HC 37> has maximum number of bonds.
Atom .R<1 1>.A<HD 53> has maximum number of bonds.
Atom .R<1 1>.A<HAB 31> has maximum number of bonds.
Atom .R<1 1>.A<HAC 47> has maximum number of bonds.
Atom .R<1 1>.A<HA 64> has maximum number of bonds.
Atom .R<1 1>.A<CMA 15> has maximum number of bonds.
Atom .R<1 1>.A<CMA 15> has maximum number of bonds.
Atom .R<1 1>.A<HA 64> has maximum number of bonds.
Atom .R<1 1>.A<HBD2 70> has maximum number of bonds.
Atom .R<1 1>.A<HBD1 69> has maximum number of bonds.
Atom .R<1 1>.A<HMA3 18> has maximum number of bonds.
Atom .R<1 1>.A<HMA1 16> has maximum number of bonds.
Atom .R<1 1>.A<O1A 12> has maximum number of bonds.
Atom .R<1 1>.A<O2A 13> has maximum number of bonds.
Atom .R<1 1>.A<O1D 72> has maximum number of bonds.
Atom .R<1 1>.A<O2D 73> has maximum number of bonds.
Atom .R<1 1>.A<C2C 40> has maximum number of bonds.
Atom .R<1 1>.A<C2D 56> has maximum number of bonds.
Atom .R<1 1>.A<CMD 57> has maximum number of bonds.
Atom .R<1 1>.A<CMC 41> has maximum number of bonds.
Atom .R<1 1>.A<C2B 24> has maximum number of bonds.
Atom .R<1 1>.A<HBC1 49> has maximum number of bonds.
Atom .R<1 1>.A<HBB1 33> has maximum number of bonds.
Atom .R<1 1>.A<C4B 35> has maximum number of bonds.
Atom .R<1 1>.A<C4C 51> has maximum number of bonds.
Atom .R<1 1>.A<CMB 25> has maximum number of bonds.
Atom .R<1 1>.A<CGA 11> has maximum number of bonds.
Atom .R<1 1>.A<CGA 11> has maximum number of bonds.
Atom .R<1 1>.A<CGD 71> has maximum number of bonds.
Atom .R<1 1>.A<CGD 71> has maximum number of bonds.
Atom .R<1 1>.A<CAD 65> has maximum number of bonds.
Atom .R<1 1>.A<C3B 29> has maximum number of bonds.
Atom .R<1 1>.A<C3D 61> has maximum number of bonds.
Atom .R<1 1>.A<C3C 45> has maximum number of bonds.
Atom .R<1 1>.A<C4A 19> has maximum number of bonds.
Atom .R<1 1>.A<HBA2 10> has maximum number of bonds.
Atom .R<1 1>.A<HBD2 70> has maximum number of bonds.
Atom .R<1 1>.A<HBD1 69> has maximum number of bonds.
Atom .R<1 1>.A<HBA1 9> has maximum number of bonds.
Atom .R<1 1>.A<HB 21> has maximum number of bonds.
Atom .R<1 1>.A<HD 53> has maximum number of bonds.
Atom .R<1 1>.A<HA 64> has maximum number of bonds.
Atom .R<1 1>.A<HC 37> has maximum number of bonds.
Atom .R<1 1>.A<CHB 20> has maximum number of bonds.
Atom .R<1 1>.A<CAC 46> has maximum number of bonds.
Atom .R<1 1>.A<CAB 30> has maximum number of bonds.
Atom .R<1 1>.A<CHA 63> has maximum number of bonds.
Atom .R<1 1>.A<CHA 63> has maximum number of bonds.
Atom .R<1 1>.A<CHA 63> has maximum number of bonds.
Atom .R<1 1>.A<ND 55> has maximum number of bonds.
Atom .R<1 1>.A<HD 53> has maximum number of bonds.
Atom .R<1 1>.A<HC 37> has maximum number of bonds.
Atom .R<1 1>.A<C3A 14> has maximum number of bonds.
Atom .R<1 1>.A<HBD2 70> has maximum number of bonds.
Atom .R<1 1>.A<HBD1 69> has maximum number of bonds.
Atom .R<1 1>.A<C3A 14> has maximum number of bonds.
Atom .R<1 1>.A<HAA2 7> has maximum number of bonds.
Atom .R<1 1>.A<HAD2 67> has maximum number of bonds.
Atom .R<1 1>.A<HAD1 66> has maximum number of bonds.
Atom .R<1 1>.A<HAA1 6> has maximum number of bonds.
Atom .R<1 1>.A<HB 21> has maximum number of bonds.
Atom .R<1 1>.A<HAC 47> has maximum number of bonds.
Atom .R<1 1>.A<HAB 31> has maximum number of bonds.
Atom .R<1 1>.A<HMA3 18> has maximum number of bonds.
Atom .R<1 1>.A<HMD3 60> has maximum number of bonds.
Atom .R<1 1>.A<HMB3 28> has maximum number of bonds.
Atom .R<1 1>.A<HMC3 44> has maximum number of bonds.
Atom .R<1 1>.A<HMC1 42> has maximum number of bonds.
Atom .R<1 1>.A<HMB1 26> has maximum number of bonds.
Atom .R<1 1>.A<HMD1 58> has maximum number of bonds.
Atom .R<1 1>.A<HMA1 16> has maximum number of bonds.
Atom .R<1 1>.A<CAD 65> has maximum number of bonds.
Atom .R<1 1>.A<NC 39> has maximum number of bonds.
Atom .R<1 1>.A<ND 55> has maximum number of bonds.
Atom .R<1 1>.A<NB 23> has maximum number of bonds.
Atom .R<1 1>.A<HAC 47> has maximum number of bonds.
Atom .R<1 1>.A<HAB 31> has maximum number of bonds.
Atom .R<1 1>.A<C1B 22> has maximum number of bonds.
Atom .R<1 1>.A<CBD 68> has maximum number of bonds.
Atom .R<1 1>.A<C3A 14> has maximum number of bonds.
Atom .R<1 1>.A<O2A 13> has maximum number of bonds.
Atom .R<1 1>.A<O1A 12> has maximum number of bonds.
Atom .R<1 1>.A<O2D 73> has maximum number of bonds.
Atom .R<1 1>.A<O1D 72> has maximum number of bonds.
)nexpected EOF: discarding residue (
!FATAL ERROR----------------------------------------
!FATAL: In file [varArray.c], line 156
!FATAL: Message: VarArrayDestroy: VARARRAY is NULL!
!ABORTING.
How can I know that the error is because of the hem_ryd.in file itself or
my pdb file?
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Received on Mon Jun 18 2012 - 06:30:03 PDT
