[gmx-users] NME ACE
David van der Spoel
spoel at xray.bmc.uu.se
Tue Nov 11 16:27:01 CET 2003
On Tue, 2003-11-11 at 16:17, Raghunadha Reddy Burri wrote:
> 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
>
you have to add the -ter option to pdb2gmx for interactive selection of
termini, then select none By default pdb2gmx adds NH3+ and COO- to your
protein.
> (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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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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