Thanks for reply.
when I tried to save to topology file and coordinate file, following message
appears. It didn't create any topology file. what will be the possible
reason for this error.I recently searched the previous messages in the
mailing list to look for solution but I found no luck.
I will be grateful for your suggestion.
chemistry.chemistry-desktop:~/Desktop$ tleap
-I: Adding /home/chemistry/amber12/dat/leap/prep to search path.
-I: Adding /home/chemistry/amber12/dat/leap/lib to search path.
-I: Adding /home/chemistry/amber12/dat/leap/parm to search path.
-I: Adding /home/chemistry/amber12/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff99SB
----- Source: /home/chemistry/amber12/dat/leap/cmd/leaprc.ff99SB
----- Source of /home/chemistry/amber12/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /home/chemistry/amber12/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /home/chemistry/amber12/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /home/chemistry/amber12/dat/leap/lib/all_nucleic94.lib
Loading library: /home/chemistry/amber12/dat/leap/lib/all_amino94.lib
Loading library: /home/chemistry/amber12/dat/leap/lib/all_aminoct94.lib
Loading library: /home/chemistry/amber12/dat/leap/lib/all_aminont94.lib
Loading library: /home/chemistry/amber12/dat/leap/lib/ions94.lib
Loading library: /home/chemistry/amber12/dat/leap/lib/solvents.lib
> loadamberparams parm99_mod.dat
Loading parameters: ./parm99_mod.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
> loadamberparams heme.frcmod
Loading parameters: ./heme.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadamberprep heme_all.in
Loading Prep file: ./heme_all.in
(no charges read on atoms lines in Heme residue ALL ATOM, Yves names,
Bayly-modified)
> heme=loadpdb oxopholrin_his.pdb
Loading PDB file: ./oxopholrin_his.pdb
-- residue 27: duplicate [ O] atoms (total 2)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Unknown residue: number: 2 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Created a new atom named: HN within residue: .R<NHID 25>
Created a new atom named: HB1 within residue: .R<NHID 25>
Created a new atom named: H1 within residue: .R<HEM 26>
Created a new atom named: H2 within residue: .R<HEM 26>
Created a new atom named: O3 within residue: .R<HEM 26>
Created a new atom named: H4 within residue: .R<HEM 26>
Created a new atom named: H5 within residue: .R<HEM 26>
Created a new atom named: H6 within residue: .R<HEM 26>
Created a new atom named: H7 within residue: .R<HEM 26>
Created a new atom named: H8 within residue: .R<HEM 26>
Created a new atom named: H9 within residue: .R<HEM 26>
Created a new atom named: H10 within residue: .R<HEM 26>
Created a new atom named: H11 within residue: .R<HEM 26>
Created a new atom named: H12 within residue: .R<HEM 26>
Created a new atom named: H13 within residue: .R<HEM 26>
Created a new atom named: H14 within residue: .R<HEM 26>
Created a new atom named: H15 within residue: .R<HEM 26>
Created a new atom named: H16 within residue: .R<HEM 26>
Created a new atom named: H17 within residue: .R<HEM 26>
Created a new atom named: H18 within residue: .R<HEM 26>
Created a new atom named: H19 within residue: .R<HEM 26>
Created a new atom named: H20 within residue: .R<HEM 26>
Created a new atom named: H21 within residue: .R<HEM 26>
Created a new atom named: H22 within residue: .R<HEM 26>
Created a new atom named: H23 within residue: .R<HEM 26>
Created a new atom named: H24 within residue: .R<HEM 26>
Created a new atom named: H25 within residue: .R<HEM 26>
Created a new atom named: H26 within residue: .R<HEM 26>
Created a new atom named: H27 within residue: .R<HEM 26>
Created a new atom named: H28 within residue: .R<HEM 26>
Created a new atom named: H29 within residue: .R<HEM 26>
Created a new atom named: H30 within residue: .R<HEM 26>
Creating new UNIT for residue: sequence: 27
Created a new atom named: O within residue: .R< 27>
total atoms in file: 92
Leap added 34 missing atoms according to residue templates:
34 H / lone pairs
The file contained 33 atoms not in residue templates
> saveamberparm heme parmtop parmcrd
Checking Unit.
WARNING: There is a bond of 6.623484 angstroms between:
------- .R<NHID 25>.A<C 18> and .R<HEM 26>.A<FE 1>
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
FATAL: Atom .R<NHID 25>.A<HN 20> does not have a type.
FATAL: Atom .R<NHID 25>.A<HB1 21> does not have a type.
FATAL: Atom .R<HEM 26>.A<H1 74> does not have a type.
FATAL: Atom .R<HEM 26>.A<H2 75> does not have a type.
FATAL: Atom .R<HEM 26>.A<O3 76> does not have a type.
FATAL: Atom .R<HEM 26>.A<H4 77> does not have a type.
FATAL: Atom .R<HEM 26>.A<H5 78> does not have a type.
FATAL: Atom .R<HEM 26>.A<H6 79> does not have a type.
FATAL: Atom .R<HEM 26>.A<H7 80> does not have a type.
FATAL: Atom .R<HEM 26>.A<H8 81> does not have a type.
FATAL: Atom .R<HEM 26>.A<H9 82> does not have a type.
FATAL: Atom .R<HEM 26>.A<H10 83> does not have a type.
FATAL: Atom .R<HEM 26>.A<H11 84> does not have a type.
FATAL: Atom .R<HEM 26>.A<H12 85> does not have a type.
FATAL: Atom .R<HEM 26>.A<H13 86> does not have a type.
FATAL: Atom .R<HEM 26>.A<H14 87> does not have a type.
FATAL: Atom .R<HEM 26>.A<H15 88> does not have a type.
FATAL: Atom .R<HEM 26>.A<H16 89> does not have a type.
FATAL: Atom .R<HEM 26>.A<H17 90> does not have a type.
FATAL: Atom .R<HEM 26>.A<H18 91> does not have a type.
FATAL: Atom .R<HEM 26>.A<H19 92> does not have a type.
FATAL: Atom .R<HEM 26>.A<H20 93> does not have a type.
FATAL: Atom .R<HEM 26>.A<H21 94> does not have a type.
FATAL: Atom .R<HEM 26>.A<H22 95> does not have a type.
FATAL: Atom .R<HEM 26>.A<H23 96> does not have a type.
FATAL: Atom .R<HEM 26>.A<H24 97> does not have a type.
FATAL: Atom .R<HEM 26>.A<H25 98> does not have a type.
FATAL: Atom .R<HEM 26>.A<H26 99> does not have a type.
FATAL: Atom .R<HEM 26>.A<H27 100> does not have a type.
FATAL: Atom .R<HEM 26>.A<H28 101> does not have a type.
FATAL: Atom .R<HEM 26>.A<H29 102> does not have a type.
FATAL: Atom .R<HEM 26>.A<H30 103> does not have a type.
FATAL: Atom .R< 27>.A<O 1> does not have a type.
Failed to generate parameters
Parameter file was not saved.
>
thanks for your answer.
fatemeh
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 22 2014 - 00:30:02 PST
