[gmx-users] Vacuum Simulation Alanine Dipeptide =>minimisation: ERROR "No default Ryckaert-Bell. types"
M. Emal Alekozai
memala at gmx.net
Thu Aug 21 23:26:00 CEST 2008
Hi,
to create some toy data I want to do a vacuum simulation of alanine dipeptide with Gromacs.
I used charmm ("generate" command) to build the structure of alanine dipeptide.
The structure in "charmm notation" is "ACE-ALA-CT3" and in "gromacs notation" is "ACE-ALA-NAC" .
The charmm output is a pdb (in charmm dialect) of alanine dipeptide [see 1].
I looked up the notation in the corresponding OPLS-force field file "/usr/share/gromacs/top/ffoplsaa.rtp" and adjusted it in the pdb file [see 2].
To convert it to a gro file I used following command:
$pdb2gmx -ter -f alanineDipeptide_gromacsOplsForceField.pdb -p alanineDipeptide_gromacsOplsForceField.top -o alanineDipeptide_gromacsOplsForceField.gro
I selected the "OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)" and
as a "N-terminus" and a "C-terminus" I selected "None".
The output gro file is [3].
For the energy minimisation I use a sample vaccum script from David van der Spoel from:
"Gromacs course in 2004 -> Gromacs exercises"
https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html
https://extras.csc.fi/chem/courses/gmx2004/exercises/exercise.tgz
When I run the grompp command I get the error message "No default Ryckaert-Bell" (see [4] for full output):
$grompp -v -zero -f energyMinimisation_steepSimple.mdp -c alanineDipeptide_gromacsOplsForceField.gro -p alanineDipeptide_gromacsOplsForceField.top -o alanineDipeptide_energyMinimisation.tpr
The corresponding topology file "alanineDipeptide_gromacsOplsForceField.top" is attached.
What do I have to adjust to get rid of the error message?
Thanks
Emal
=====1. PDB IN CHARMM DIALECT
REMARK COORDINATES FOR FRAGMENT/ PEPTIDE WITH TERMINI
REMARK DATE: 8/20/ 8 1: 4: 7 CREATED BY USER: emal
ATOM 1 CAY ALA 1 -10.138 -4.600 4.190 1.00 0.00 ALAD
ATOM 2 HY1 ALA 1 -11.149 -4.333 3.817 1.00 0.00 ALAD
ATOM 3 HY2 ALA 1 -9.523 -4.958 3.336 1.00 0.00 ALAD
ATOM 4 HY3 ALA 1 -9.654 -3.701 4.627 1.00 0.00 ALAD
ATOM 5 CY ALA 1 -10.229 -5.671 5.206 1.00 0.00 ALAD
ATOM 6 OY ALA 1 -9.447 -6.612 5.208 1.00 0.00 ALAD
ATOM 7 N ALA 1 -11.211 -5.565 6.107 1.00 0.00 ALAD
ATOM 8 HN ALA 1 -11.843 -4.801 6.075 1.00 0.00 ALAD
ATOM 9 CA ALA 1 -11.421 -6.529 7.170 1.00 0.00 ALAD
ATOM 10 HA ALA 1 -10.458 -6.861 7.536 1.00 0.00 ALAD
ATOM 11 CB ALA 1 -12.168 -5.848 8.335 1.00 0.00 ALAD
ATOM 12 HB1 ALA 1 -12.307 -6.558 9.179 1.00 0.00 ALAD
ATOM 13 HB2 ALA 1 -13.171 -5.499 8.007 1.00 0.00 ALAD
ATOM 14 HB3 ALA 1 -11.590 -4.974 8.702 1.00 0.00 ALAD
ATOM 15 C ALA 1 -12.172 -7.778 6.699 1.00 0.00 ALAD
ATOM 16 O ALA 1 -13.319 -8.018 7.067 1.00 0.00 ALAD
ATOM 17 NT ALA 1 -11.511 -8.601 5.861 1.00 0.00 ALAD
ATOM 18 HNT ALA 1 -10.598 -8.316 5.559 1.00 0.00 ALAD
ATOM 19 CAT ALA 1 -12.058 -9.831 5.329 1.00 0.00 ALAD
ATOM 20 HT1 ALA 1 -13.146 -9.935 5.547 1.00 0.00 ALAD
ATOM 21 HT2 ALA 1 -11.927 -9.864 4.225 1.00 0.00 ALAD
ATOM 22 HT3 ALA 1 -11.534 -10.708 5.770 1.00 0.00 ALAD
TER 23 ALA 1
END
=====2. PDB IN GROMACS DIALECT
REMARK COORDINATES FOR FRAGMENT/ PEPTIDE WITH TERMINI
REMARK DATE: 8/20/ 8 1: 4: 7 CREATED BY USER: emal
ATOM 1 CH3 ACE 1 -10.138 -4.600 4.190 1.00 0.00
ATOM 2 HH31 ACE 1 -11.149 -4.333 3.817 1.00 0.00
ATOM 3 HH32 ACE 1 -9.523 -4.958 3.336 1.00 0.00
ATOM 4 HH33 ACE 1 -9.654 -3.701 4.627 1.00 0.00
ATOM 5 C ACE 1 -10.229 -5.671 5.206 1.00 0.00
ATOM 6 O ACE 1 -9.447 -6.612 5.208 1.00 0.00
ATOM 7 N ALA 2 -11.211 -5.565 6.107 1.00 0.00
ATOM 8 H ALA 2 -11.843 -4.801 6.075 1.00 0.00
ATOM 9 CA ALA 2 -11.421 -6.529 7.170 1.00 0.00
ATOM 10 HA ALA 2 -10.458 -6.861 7.536 1.00 0.00
ATOM 11 CB ALA 2 -12.168 -5.848 8.335 1.00 0.00
ATOM 12 HB1 ALA 2 -12.307 -6.558 9.179 1.00 0.00
ATOM 13 HB2 ALA 2 -13.171 -5.499 8.007 1.00 0.00
ATOM 14 HB3 ALA 2 -11.590 -4.974 8.702 1.00 0.00
ATOM 15 C ALA 2 -12.172 -7.778 6.699 1.00 0.00
ATOM 16 O ALA 2 -13.319 -8.018 7.067 1.00 0.00
ATOM 17 N NAC 3 -11.511 -8.601 5.861 1.00 0.00
ATOM 18 H NAC 3 -10.598 -8.316 5.559 1.00 0.00
ATOM 19 CH3 NAC 3 -12.058 -9.831 5.329 1.00 0.00
ATOM 20 HH31 NAC 3 -13.146 -9.935 5.547 1.00 0.00
ATOM 21 HH32 NAC 3 -11.927 -9.864 4.225 1.00 0.00
ATOM 22 HH33 NAC 3 -11.534 -10.708 5.770 1.00 0.00
TER
END
=====3. GRO FILE
God Rules Over Mankind, Animals, Cosmos and Such
22
1ACE CH3 1 -1.014 -0.460 0.419
1ACE HH31 2 -1.115 -0.433 0.382
1ACE HH32 3 -0.952 -0.496 0.334
1ACE HH33 4 -0.965 -0.370 0.463
1ACE C 5 -1.023 -0.567 0.521
1ACE O 6 -0.945 -0.661 0.521
2ALA N 7 -1.121 -0.557 0.611
2ALA H 8 -1.184 -0.480 0.608
2ALA CA 9 -1.142 -0.653 0.717
2ALA HA 10 -1.046 -0.686 0.754
2ALA CB 11 -1.217 -0.585 0.834
2ALA HB1 12 -1.231 -0.656 0.918
2ALA HB2 13 -1.317 -0.550 0.801
2ALA HB3 14 -1.159 -0.497 0.870
2ALA C 15 -1.217 -0.778 0.670
2ALA O 16 -1.332 -0.802 0.707
3NAC N 17 -1.151 -0.860 0.586
3NAC H 18 -1.060 -0.832 0.556
3NAC CH3 19 -1.206 -0.983 0.533
3NAC HH31 20 -1.315 -0.993 0.555
3NAC HH32 21 -1.193 -0.986 0.423
3NAC HH33 22 -1.153 -1.071 0.577
0.38720 0.70070 0.58430
=====4. GROMPP OUTPUT
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
WARNING 1 [file energyMinimisation_b4emVaccum.mdp, line unknown]:
Unknown left-hand 'bd-temp' in parameter file
checking input for internal consistency...
WARNING 2 [file energyMinimisation_b4emVaccum.mdp, line unknown]:
Can only use nstype=Simple with pbc=no, setting nstype to Simple
WARNING 3 [file energyMinimisation_b4emVaccum.mdp, line unknown]:
For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
ERROR 3 [file "alanineDipeptide_gromacsOplsForceField.top", line 158]:
No default Ryckaert-Bell. types
ERROR 3 [file "alanineDipeptide_gromacsOplsForceField.top", line 183]:
No default Ryckaert-Bell. types
Excluding 3 bonded neighbours for Protein 1
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
# BONDS: 21
# ANGLES: 36
# PDIHS: 4
# RBDIHS: 22
# LJ14: 41
There were 3 warnings
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/grompp.c, line: 1207
Fatal error:
There were 2 errors in input file(s)
-------------------------------------------------------
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