Hi all,
While performing MD on DNA, I am using steps as follows:
Step 1-
mkdir dna
Step 2-
cd dna
Step 3-
Wget “link”
Step 4-
Ls
DNA.pdb (which was downloaded from scfbio DNA Sequence to Structure tool)
Step 5-
Cp DNA.pdb complex.pdb
Step 6-
[pradeep.coe dna]$ tleap
Ø var = loadpdb complex.pdb
-I: Adding /opt/apps/amber/10/openmpi-mkl/dat/leap/prep to search path.
-I: Adding /opt/apps/amber/10/openmpi-mkl/dat/leap/lib to search path.
-I: Adding /opt/apps/amber/10/openmpi-mkl/dat/leap/parm to search path.
-I: Adding /opt/apps/amber/10/openmpi-mkl/dat/leap/cmd to search path.
Welcome to LEaP!
Sourcing leaprc: /opt/apps/amber/10/openmpi-mkl/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters: /opt/apps/amber/10/openmpi-mkl/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters:
/opt/apps/amber/10/openmpi-mkl/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library:
/opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_nucleic94.lib
Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_amino94.lib
Loading library:
/opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_aminoct94.lib
Loading library:
/opt/apps/amber/10/openmpi-mkl/dat/leap/lib/all_aminont94.lib
Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/ions94.lib
Loading library: /opt/apps/amber/10/openmpi-mkl/dat/leap/lib/solvents.lib
Ø >Created a new atom named: 2H2 within residue: .R<DG 8>
Ø Created a new atom named: 1H5 within residue: .R<DC 9>
Ø Created a new atom named: 2H5 within residue: .R<DC 9>
Ø Created a new atom named: 1H2 within residue: .R<DC 9>
Ø Created a new atom named: 2H2 within residue: .R<DC 9>
Ø Created a new atom named: 1H4 within residue: .R<DC 9>
Ø Created a new atom named: 2H4 within residue: .R<DC 9>
Ø Created a new atom named: 1H5 within residue: .R<DG 10>
Ø Created a new atom named: 2H5 within residue: .R<DG 10>
Ø Created a new atom named: 1H2 within residue: .R<DG 10>
Ø Created a new atom named: 2H2 within residue: .R<DG 10>
Ø Created a new atom named: 1H5 within residue: .R<DC 11>
Ø Created a new atom named: 2H5 within residue: .R<DC 11>
Ø Created a new atom named: 1H2 within residue: .R<DC 11>
Ø Created a new atom named: 2H2 within residue: .R<DC 11>
Ø Created a new atom named: 1H4 within residue: .R<DC 11>
Ø Created a new atom named: 2H4 within residue: .R<DC 11>
Ø Created a new atom named: 1H5 within residue: .R<DC 12>
Ø Created a new atom named: 2H5 within residue: .R<DC 12>
Ø Created a new atom named: 1H2 within residue: .R<DC 12>
Ø Created a new atom named: 2H2 within residue: .R<DC 12>
Ø Created a new atom named: 1H4 within residue: .R<DC 12>
Ø Created a new atom named: 2H4 within residue: .R<DC 12>
Ø Created a new atom named: 1H5 within residue: .R<DC 13>
Ø Created a new atom named: 2H5 within residue: .R<DC 13>
Ø Created a new atom named: 1H2 within residue: .R<DC 13>
Ø Created a new atom named: 2H2 within residue: .R<DC 13>
Ø Created a new atom named: 1H4 within residue: .R<DC 13>
Ø Created a new atom named: 2H4 within residue: .R<DC 13>
Ø Created a new atom named: 1H5 within residue: .R<DC 14>
Ø Created a new atom named: 2H5 within residue: .R<DC 14>
Ø Created a new atom named: 1H2 within residue: .R<DC 14>
Ø Created a new atom named: 2H2 within residue: .R<DC 14>
Ø Created a new atom named: 1H4 within residue: .R<DC 14>
Ø Created a new atom named: 2H4 within residue: .R<DC 14>
Ø Created a new atom named: 1H5 within residue: .R<DT 15>
Ø Created a new atom named: 2H5 within residue: .R<DT 15>
Ø Created a new atom named: 1H2 within residue: .R<DT 15>
Ø Created a new atom named: 2H2 within residue: .R<DT 15>
Ø Created a new atom named: 3H5 within residue: .R<DT 15>
Ø Created a new atom named: 1H5 within residue: .R<DT 16>
Ø Created a new atom named: 2H5 within residue: .R<DT 16>
Ø Created a new atom named: 1H2 within residue: .R<DT 16>
Ø Created a new atom named: 2H2 within residue: .R<DT 16>
Ø Created a new atom named: 3H5 within residue: .R<DT 16>
Ø Created a new atom named: 1H5 within residue: .R<DA 17>
Ø Created a new atom named: 2H5 within residue: .R<DA 17>
Ø Created a new atom named: 1H2 within residue: .R<DA 17>
Ø Created a new atom named: 2H2 within residue: .R<DA 17>
Ø Created a new atom named: 1H6 within residue: .R<DA 17>
Ø Created a new atom named: 2H6 within residue: .R<DA 17>
Ø Created a new atom named: 1H5 within residue: .R<DG 18>
Ø Created a new atom named: 2H5 within residue: .R<DG 18>
Ø Created a new atom named: 1H2 within residue: .R<DG 18>
Ø Created a new atom named: 2H2 within residue: .R<DG 18>
Ø Created a new atom named: 1H5 within residue: .R<DG 19>
Ø Created a new atom named: 2H5 within residue: .R<DG 19>
Ø Created a new atom named: 1H2 within residue: .R<DG 19>
Ø Created a new atom named: 2H2 within residue: .R<DG 19>
Ø Created a new atom named: 1H5 within residue: .R<DG 20>
Ø Created a new atom named: 2H5 within residue: .R<DG 20>
Ø Created a new atom named: 1H2 within residue: .R<DG 20>
Ø Created a new atom named: 2H2 within residue: .R<DG 20>
Ø Created a new atom named: 1H5 within residue: .R<DG 21>
Ø Created a new atom named: 2H5 within residue: .R<DG 21>
Ø Created a new atom named: 1H2 within residue: .R<DG 21>
Ø Created a new atom named: 2H2 within residue: .R<DG 21>
Ø Created a new atom named: 1H5 within residue: .R<DC 22>
Ø Created a new atom named: 2H5 within residue: .R<DC 22>
Ø Created a new atom named: 1H2 within residue: .R<DC 22>
Ø Created a new atom named: 2H2 within residue: .R<DC 22>
Ø Created a new atom named: 1H4 within residue: .R<DC 22>
Ø Created a new atom named: 2H4 within residue: .R<DC 22>
Ø Created a new atom named: 1H5 within residue: .R<DC 23>
Ø Created a new atom named: 2H5 within residue: .R<DC 23>
Ø Created a new atom named: 1H2 within residue: .R<DC 23>
Ø Created a new atom named: 2H2 within residue: .R<DC 23>
Ø Created a new atom named: 1H4 within residue: .R<DC 23>
Ø Created a new atom named: 2H4 within residue: .R<DC 23>
Ø Created a new atom named: 1H5 within residue: .R<DA 24>
Ø Created a new atom named: 2H5 within residue: .R<DA 24>
Ø Created a new atom named: 1H2 within residue: .R<DA 24>
Ø Created a new atom named: 2H2 within residue: .R<DA 24>
Ø Created a new atom named: 1H6 within residue: .R<DA 24>
Ø Created a new atom named: 2H6 within residue: .R<DA 24>
Ø Created a new atom named: 1H5 within residue: .R<DA3 25>
Ø Created a new atom named: 2H5 within residue: .R<DA3 25>
Ø Created a new atom named: 1H2 within residue: .R<DA3 25>
Ø Created a new atom named: 2H2 within residue: .R<DA3 25>
Ø Created a new atom named: 1H6 within residue: .R<DA3 25>
Ø Created a new atom named: 2H6 within residue: .R<DA3 25>
Ø Created a new atom named: 1H5 within residue: .R<DT5 26>
Ø Created a new atom named: 2H5 within residue: .R<DT5 26>
Ø Created a new atom named: 1H2 within residue: .R<DT5 26>
Ø Created a new atom named: 2H2 within residue: .R<DT5 26>
Ø Created a new atom named: 3H5 within residue: .R<DT5 26>
Ø Created a new atom named: 1H5 within residue: .R<DT 27>
Ø Created a new atom named: 2H5 within residue: .R<DT 27>
Ø Created a new atom named: 1H2 within residue: .R<DT 27>
Ø Created a new atom named: 2H2 within residue: .R<DT 27>
Ø Created a new atom named: 3H5 within residue: .R<DT 27>
Ø Created a new atom named: 1H5 within residue: .R<DG 28>
Ø Created a new atom named: 2H5 within residue: .R<DG 28>
Ø Created a new atom named: 1H2 within residue: .R<DG 28>
Ø Created a new atom named: 2H2 within residue: .R<DG 28>
Ø Created a new atom named: 1H5 within residue: .R<DG 29>
Ø Created a new atom named: 2H5 within residue: .R<DG 29>
Ø Created a new atom named: 1H2 within residue: .R<DG 29>
Ø Created a new atom named: 2H2 within residue: .R<DG 29>
Ø Created a new atom named: 1H5 within residue: .R<DC 30>
Ø Created a new atom named: 2H5 within residue: .R<DC 30>
Ø Created a new atom named: 1H2 within residue: .R<DC 30>
Ø Created a new atom named: 2H2 within residue: .R<DC 30>
Ø Created a new atom named: 1H4 within residue: .R<DC 30>
Ø Created a new atom named: 2H4 within residue: .R<DC 30>
Ø Created a new atom named: 1H5 within residue: .R<DC 31>
Ø Created a new atom named: 2H5 within residue: .R<DC 31>
Ø Created a new atom named: 1H2 within residue: .R<DC 31>
Ø Created a new atom named: 2H2 within residue: .R<DC 31>
Ø Created a new atom named: 1H4 within residue: .R<DC 31>
Ø Created a new atom named: 2H4 within residue: .R<DC 31>
Ø Created a new atom named: 1H5 within residue: .R<DC 32>
Ø Created a new atom named: 2H5 within residue: .R<DC 32>
Ø Created a new atom named: 1H2 within residue: .R<DC 32>
Ø Created a new atom named: 2H2 within residue: .R<DC 32>
Ø Created a new atom named: 1H4 within residue: .R<DC 32>
Ø Created a new atom named: 2H4 within residue: .R<DC 32>
Ø Created a new atom named: 1H5 within residue: .R<DC 33>
Ø Created a new atom named: 2H5 within residue: .R<DC 33>
Ø Created a new atom named: 1H2 within residue: .R<DC 33>
Ø Created a new atom named: 2H2 within residue: .R<DC 33>
Ø Created a new atom named: 1H4 within residue: .R<DC 33>
Ø Created a new atom named: 2H4 within residue: .R<DC 33>
Ø Created a new atom named: 1H5 within residue: .R<DT 34>
Ø Created a new atom named: 2H5 within residue: .R<DT 34>
Ø Created a new atom named: 1H2 within residue: .R<DT 34>
Ø Created a new atom named: 2H2 within residue: .R<DT 34>
Ø Created a new atom named: 3H5 within residue: .R<DT 34>
Ø Created a new atom named: 1H5 within residue: .R<DA 35>
Ø Created a new atom named: 2H5 within residue: .R<DA 35>
Ø Created a new atom named: 1H2 within residue: .R<DA 35>
Ø Created a new atom named: 2H2 within residue: .R<DA 35>
Ø Created a new atom named: 1H6 within residue: .R<DA 35>
Ø Created a new atom named: 2H6 within residue: .R<DA 35>
Ø Created a new atom named: 1H5 within residue: .R<DA 36>
Ø Created a new atom named: 2H5 within residue: .R<DA 36>
Ø Created a new atom named: 1H2 within residue: .R<DA 36>
Ø Created a new atom named: 2H2 within residue: .R<DA 36>
Ø Created a new atom named: 1H6 within residue: .R<DA 36>
Ø Created a new atom named: 2H6 within residue: .R<DA 36>
Ø Created a new atom named: 1H5 within residue: .R<DG 37>
Ø Created a new atom named: 2H5 within residue: .R<DG 37>
Ø Created a new atom named: 1H2 within residue: .R<DG 37>
Ø Created a new atom named: 2H2 within residue: .R<DG 37>
Ø Created a new atom named: 1H5 within residue: .R<DG 38>
Ø Created a new atom named: 2H5 within residue: .R<DG 38>
Ø Created a new atom named: 1H2 within residue: .R<DG 38>
Ø Created a new atom named: 2H2 within residue: .R<DG 38>
Ø Created a new atom named: 1H5 within residue: .R<DG 39>
Ø Created a new atom named: 2H5 within residue: .R<DG 39>
Ø Created a new atom named: 1H2 within residue: .R<DG 39>
Ø Created a new atom named: 2H2 within residue: .R<DG 39>
Ø Created a new atom named: 1H5 within residue: .R<DG 40>
Ø Created a new atom named: 2H5 within residue: .R<DG 40>
Ø Created a new atom named: 1H2 within residue: .R<DG 40>
Ø Created a new atom named: 2H2 within residue: .R<DG 40>
Ø Created a new atom named: 1H5 within residue: .R<DC 41>
Ø Created a new atom named: 2H5 within residue: .R<DC 41>
Ø Created a new atom named: 1H2 within residue: .R<DC 41>
Ø Created a new atom named: 2H2 within residue: .R<DC 41>
Ø Created a new atom named: 1H4 within residue: .R<DC 41>
Ø Created a new atom named: 2H4 within residue: .R<DC 41>
Ø Created a new atom named: 1H5 within residue: .R<DG 42>
Ø Created a new atom named: 2H5 within residue: .R<DG 42>
Ø Created a new atom named: 1H2 within residue: .R<DG 42>
Ø Created a new atom named: 2H2 within residue: .R<DG 42>
Ø Created a new atom named: 1H5 within residue: .R<DC 43>
Ø Created a new atom named: 2H5 within residue: .R<DC 43>
Ø Created a new atom named: 1H2 within residue: .R<DC 43>
Ø Created a new atom named: 2H2 within residue: .R<DC 43>
Ø Created a new atom named: 1H4 within residue: .R<DC 43>
Ø Created a new atom named: 2H4 within residue: .R<DC 43>
Ø Created a new atom named: 1H5 within residue: .R<DA 44>
Ø Created a new atom named: 2H5 within residue: .R<DA 44>
Ø Created a new atom named: 1H2 within residue: .R<DA 44>
Ø Created a new atom named: 2H2 within residue: .R<DA 44>
Ø Created a new atom named: 1H6 within residue: .R<DA 44>
Ø Created a new atom named: 2H6 within residue: .R<DA 44>
Ø Created a new atom named: 1H5 within residue: .R<DG 45>
Ø Created a new atom named: 2H5 within residue: .R<DG 45>
Ø Created a new atom named: 1H2 within residue: .R<DG 45>
Ø Created a new atom named: 2H2 within residue: .R<DG 45>
Ø Created a new atom named: 1H5 within residue: .R<DC 46>
Ø Created a new atom named: 2H5 within residue: .R<DC 46>
Ø Created a new atom named: 1H2 within residue: .R<DC 46>
Ø Created a new atom named: 2H2 within residue: .R<DC 46>
Ø Created a new atom named: 1H4 within residue: .R<DC 46>
Ø Created a new atom named: 2H4 within residue: .R<DC 46>
Ø Created a new atom named: 1H5 within residue: .R<DC 47>
Ø Created a new atom named: 2H5 within residue: .R<DC 47>
Ø Created a new atom named: 1H2 within residue: .R<DC 47>
Ø Created a new atom named: 2H2 within residue: .R<DC 47>
Ø Created a new atom named: 1H4 within residue: .R<DC 47>
Ø Created a new atom named: 2H4 within residue: .R<DC 47>
Ø Created a new atom named: 1H5 within residue: .R<DT 48>
Ø Created a new atom named: 2H5 within residue: .R<DT 48>
Ø Created a new atom named: 1H2 within residue: .R<DT 48>
Ø Created a new atom named: 2H2 within residue: .R<DT 48>
Ø Created a new atom named: 3H5 within residue: .R<DT 48>
Ø Created a new atom named: 1H5 within residue: .R<DT 49>
Ø Created a new atom named: 2H5 within residue: .R<DT 49>
Ø Created a new atom named: 1H2 within residue: .R<DT 49>
Ø Created a new atom named: 2H2 within residue: .R<DT 49>
Ø Created a new atom named: 3H5 within residue: .R<DT 49>
Ø Created a new atom named: 1H5 within residue: .R<DT3 50>
Ø Created a new atom named: 2H5 within residue: .R<DT3 50>
Ø Created a new atom named: 1H2 within residue: .R<DT3 50>
Ø Created a new atom named: 2H2 within residue: .R<DT3 50>
Ø Created a new atom named: 3H5 within residue: .R<DT3 50>
Ø total atoms in file: 1582
Leap added 309 missing atoms according to residue templates:
309 H / lone pairs
* The file contained 259 atoms not in residue templates*
As 259 atoms not in the residue templates, I am not able to create .prmtop
and .crd files. Please help me in resolving this problem.
Thanks,
Pradeep Pant
IIT Delhi
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 02 2014 - 04:00:02 PDT
