[gmx-users] NME ACE
Raghunadha Reddy Burri
burri at heineken.chemie.uni-dortmund.de
Tue Nov 11 16:18:01 CET 2003
Dear David and GMX users,
I have problem in pdb2gmx, please help me, this problem same as Peter Nagy
your solved In July 8th 2003.
As per your previous ( Peter Nagy) suggestions I was Changed
NME --> NAC,
CH3 --> CA
but I am getting another error like
Fatal error: atom N not found in residue 1ACE while combining tdb and rtp
(details below)
I dont want them to be protonated at two N-termini but for testing I was
replaced with N in place 1HH3 (!!!) that opens another error like
Fatal error: Residue 'CE' not found in residue topology database
I am looking forward for suggestions to overcome this problem
Thank you very much
Raghu
(Deatils below with 20 lines PDB file)
______________________
> pdb2gmx -f -ignh pep1.pdb
Read 49 atoms
Opening library file /usr/local/software/gromacs-3.1.4/top/xlateat.dat
13 out of 13 lines of xlateat.dat converted succesfully
Opening library file /usr/local/software/gromacs-3.1.4/top/aminoacids.dat
Analyzing pdb file
There are 1 chains and 0 blocks of water and 10 residues with 49 atoms
chain #res #atoms
1 ' ' 10 49
All occupancies are one
Opening library file /usr/local/software/gromacs-3.1.4/top/FF.dat
Select the Force Field:
0: Gromacs Forcefield (see manual)
1: Gromacs Forcefield with all hydrogens (proteins only)
2: GROMOS96 43a1 Forcefield (official distribution)
3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
0
Using ffgmx force field
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx.atp
Atomtype 52
Reading residue database... (ffgmx)
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx.rtp
Using default value - not generating all possible dihedrals
Using default value - excluding 3 bonded neighbors
Residue 97
Sorting it all out...
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx.hdb
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx-n.tdb
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (49 atoms, 10 residues)
Opening library file /usr/local/software/gromacs-3.1.4/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 9 donors and 9 acceptors
There are 17 hydrogen bonds
Checking for duplicate atoms....
N-terminus: NH3+
C-terminus: COO-
Now there are 10 residues with 57 atoms
Fatal error: atom N not found in residue 1ACE while combining tdb and rtp
______________________
My PDB file (Note ACE N-termin... NAC C-ter..)
ATOM 1 1HH3 ACE 1 1.328 2.173 -0.000 1.00 0.00
ATOM 2 CA ACE 1 2.006 1.318 -0.000 1.00 0.00
ATOM 3 2HH3 ACE 1 2.634 1.352 0.890 1.00 0.00
ATOM 4 3HH3 ACE 1 2.634 1.352 -0.890 1.00 0.00
ATOM 5 C ACE 1 1.229 0.000 0.000 1.00 0.00
ATOM 6 O ACE 1 0.000 0.000 0.000 1.00 0.00
ATOM 7 N GLY 2 1.954 -1.093 -0.247 1.00 0.00
ATOM 8 H GLY 2 2.963 -1.044 -0.236 1.00 0.00
ATOM 9 CA GLY 2 1.337 -2.372 -0.536 1.00 0.00
ATOM 10 HA2 GLY 2 0.717 -2.284 -1.428 1.00 0.00
.....
ATOM 93 HA2 GLY 9 3.924 -15.991 11.647 1.00 0.00
ATOM 94 HA3 GLY 9 3.155 -16.561 13.147 1.00 0.00
ATOM 95 C GLY 9 3.048 -17.939 11.512 1.00 0.00
ATOM 96 O GLY 9 2.085 -18.345 10.864 1.00 0.00
ATOM 97 N NAC 10 4.116 -18.695 11.773 1.00 0.00
ATOM 98 H NAC 10 4.883 -18.317 12.310 1.00 0.00
ATOM 99 CA NAC 10 4.219 -20.063 11.306 1.00 0.00
ATOM 100 1HH3 NAC 10 3.322 -20.325 10.746 1.00 0.00
ATOM 101 2HH3 NAC 10 5.092 -20.162 10.660 1.00 0.00
ATOM 102 3HH3 NAC 10 4.322 -20.732 12.160 1.00 0.00
TER 103 NAC 10
END
______________
just for testing I was changed 1HH3 with N
thats opened another error like this
> pdb2gmx -f -ignh pep1.pdb
Read 50 atoms
Opening library file /usr/local/software/gromacs-3.1.4/top/xlateat.dat
13 out of 13 lines of xlateat.dat converted succesfully
Opening library file /usr/local/software/gromacs-3.1.4/top/aminoacids.dat
Analyzing pdb file
There are 1 chains and 0 blocks of water and 11 residues with 50 atoms
chain #res #atoms
1 ' ' 11 50
All occupancies are one
Opening library file /usr/local/software/gromacs-3.1.4/top/FF.dat
Select the Force Field:
0: Gromacs Forcefield (see manual)
1: Gromacs Forcefield with all hydrogens (proteins only)
2: GROMOS96 43a1 Forcefield (official distribution)
3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
0
Using ffgmx force field
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx.atp
Atomtype 52
Reading residue database... (ffgmx)
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx.rtp
Using default value - not generating all possible dihedrals
Using default value - excluding 3 bonded neighbors
Residue 97
Sorting it all out...
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx.hdb
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx-n.tdb
Opening library file /usr/local/software/gromacs-3.1.4/top/ffgmx-c.tdb
Processing chain 1 (50 atoms, 11 residues)
Opening library file /usr/local/software/gromacs-3.1.4/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 10 donors and 9 acceptors
There are 18 hydrogen bonds
Fatal error: Residue 'CE' not found in residue topology database
______________________________
David L. Bostick gmx-users at gromacs.org
Tue Jul 8 22:21:02 2003
HI,
Try changing NME to NAC. I believe gmx will recognize this. It's just the
naming... check the rtp file that you are using from the /top directory to
see.
David
Dear Gromacs Users!
Following the suggestion of David Bostick (thank you, Dave), I =
changed=20
NME to NAC. There was no problem with the name ACE. The type of the =
methyl
carbons (originally appeared as CH3) had to be changed to CA, and then =
pdb2gmx
worked, producing a seemingly correct conf.gro file.
Thanks for the quick help.
Peter Nagy
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