Dear AMBER users,
I am trying to follow the tutorial: *Simulating the Green Fluorescent
Protein and building a modified amino acid residue*, for MD simulation of a
stapled peptide complex (attached).
After fragmentation, and ACE/NME capping, and charge fit with Gaussian. I
am stuck on section 2 of the above tutorial. I saved individual pdb files
for the fragments and then merged three fragments into one molecule, (one
pdb file) by following procedure discussed in section 2.
Now for MD simulation, when I went back to tleap, and I got the following
error. Could you please look, what is wrong in my final pdb file.
Thank you very much!
Best regards
Atul
*Uni. of Notre Dame*
*Error details*:
-bash-4.2$ tleap
-I: Adding /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/prep
to search path.
-I: Adding /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/lib
to search path.
-I: Adding /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/parm
to search path.
-I: Adding /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/cmd
to search path. Welcome to LEaP!
(no leaprc in search path)
> source leaprc.protein.ff14SB
----- Source: /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/cmd/leaprc.protein.ff14SB
done
Log file: ./leap.log
Loading parameters: /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/lib/amino12.lib
Loading library: /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/lib/aminoct12.lib
Loading library: /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/lib/aminont12.lib
> source leaprc.gaff
----- Source: /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/cmd/leaprc.gaff
done
Log file: ./leap.log
Loading parameters: /afs/
crc.nd.edu/x86_64_linux/a/amber/16.0/intel/17.1/ompi-2.1.1/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
> lnk = loadpdb LNK1_PEP_LNK2.pdb
Loading PDB file: ./LNK1_PEP_LNK2.pdb
-- residue 2: duplicate [ C] atoms (total 5)
-- residue 2: duplicate [ H] atoms (total 9)
-- residue 2: duplicate [ N] atoms (total 2)
-- residue 2: duplicate [ O] atoms (total 2)
-- residue 3: duplicate [ C] atoms (total 12)
-- residue 3: duplicate [ H] atoms (total 22)
-- residue 4: duplicate [ C] atoms (total 5)
-- residue 4: duplicate [ H] atoms (total 9)
-- residue 4: duplicate [ N] atoms (total 2)
-- residue 4: 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: 0 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: number: 1 type: Nonterminal
Unknown residue: number: 2 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: sequence: 2
Created a new atom named: C within residue: .R< 2>
Created a new atom named: N within residue: .R< 2>
Created a new atom named: H within residue: .R< 2>
Created a new atom named: O within residue: .R< 2>
Creating new UNIT for residue: sequence: 3
Created a new atom named: C within residue: .R< 3>
Created a new atom named: S within residue: .R< 3>
Created a new atom named: H within residue: .R< 3>
Creating new UNIT for residue: sequence: 4
Created a new atom named: C within residue: .R< 4>
Created a new atom named: N within residue: .R< 4>
Created a new atom named: H within residue: .R< 4>
Created a new atom named: O within residue: .R< 4>
Bond: maximum coordination exceeded on .R< 2>.A<H 3>
-- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R< 2>.A<H 3> .R< 2>.A<N 2>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 445
!FATAL: Message: bondAtomProblem found
!
!ABORTING.
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- application/octet-stream attachment: LNK1.pdb
- application/octet-stream attachment: PEP.pdb
- application/octet-stream attachment: LNK2.pdb
Received on Mon Dec 03 2018 - 09:00:01 PST
