Respected fellow members
Somehow in my input script I am facing a problem in reading charmm topology
file top_all27_prot_lipid.pro and hence in the execution of the script.
It would be very helpful if someone can guide me through the mistake that I
might be doing.
Thank You
Following is the error message
X-PLOR>RTFRDR> ASSFIL: file /opt/nih/xplor-nih-2.47/toppar/
top_all27_prot_lipid.pro opened.
RTFRDR>*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
%RTFRDR-ERR: unrecognized command:
*>>>>>>
^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> Combined
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> Combined CHARMM
^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> Combined CHARMM All-Hydrogen
^^^^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> Combined CHARMM All-Hydrogen Topology
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> Combined CHARMM All-Hydrogen Topology File
^^^^
%NEXTCD-ERR: Symbol expected:
*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<
^
%RTFRDR-ERR: IN expected:
*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
^^^^^^^^
FOR-clause=*>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
%RTFRDR-ERR: LOOP expected:
*>
^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>> CHARMM22
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>> CHARMM22 Proteins
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>> CHARMM22 Proteins and
^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>> CHARMM22 Proteins and CHARMM27
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids
^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
^^^^^^^^^^
RTFRDR>*from
%RTFRDR-ERR: unrecognized command:
*from
^^^^^
RTFRDR>*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>CHARMM22
^^^^^^^^^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>CHARMM22 All-Hydrogen
^^^^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>CHARMM22 All-Hydrogen Topology
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>CHARMM22 All-Hydrogen Topology File
^^^^
%NEXTCD-ERR: Symbol expected:
*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins
^^^^^^^^
%RTFRDR-ERR: IN expected:
*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
^^^^^^
FOR-clause=*>>>>>>>>>>>>>>>>>>>>> August 1999
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
%RTFRDR-ERR: LOOP expected:
*>
^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>>>>>>>>>>>>>> August
^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>>>>>>>>>>>>>> August 1999
^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RTFRDR>*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
%RTFRDR-ERR: unrecognized command:
*>>>>>>>
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>> Direct
^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>> Direct comments
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>> Direct comments to
^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>> Direct comments to Alexander
^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>> Direct comments to Alexander D.
^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>> Direct comments to Alexander D. MacKerell
^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>> Direct comments to Alexander D. MacKerell Jr.
^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
^^^^^^^^^
RTFRDR>*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
%RTFRDR-ERR: unrecognized command:
*>>>>>>
^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> 410-706-7442
^^^^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> 410-706-7442 or
^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> 410-706-7442 or email:
^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> 410-706-7442 or email:
^
%RTFRDR-ERR: unrecognized command:
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu
^^^^^^^^^^^^^^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
^^^^^^^^^
RTFRDR>*and
%RTFRDR-ERR: unrecognized command:
*and
^^^^
RTFRDR>* \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
%RTFRDR-ERR: unrecognized command:
*
^
%RTFRDR-ERR: unrecognized command:
* \\\\\\\ CHARMM27
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
* \\\\\\\ CHARMM27 All-Hydrogen
^^^^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
* \\\\\\\ CHARMM27 All-Hydrogen Lipid
^^^^^
%RTFRDR-ERR: unrecognized command:
* \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
* \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File
^^^^
%RTFRDR-ERR: unrecognized command:
* \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
^^^^^^^
RTFRDR>* \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
%RTFRDR-ERR: unrecognized command:
*
^
%RTFRDR-ERR: unrecognized command:
* \\\\\\\\\\\\\\\\\\ Developmental
^^^^^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
* \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
^^^^^^^^^^^^^^^^^^^^^^^^^
RTFRDR>* Alexander D. MacKerell Jr.
%RTFRDR-ERR: unrecognized command:
*
^
%RTFRDR-ERR: unrecognized command:
* Alexander
^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
* Alexander D.
^^
%RTFRDR-ERR: unrecognized command:
* Alexander D. MacKerell
^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
* Alexander D. MacKerell Jr.
^^^
RTFRDR>* August 1999
%RTFRDR-ERR: unrecognized command:
*
^
%RTFRDR-ERR: unrecognized command:
* August
^^^^^^
%RTFRDR-ERR: unrecognized command:
* August 1999
^^^^
RTFRDR>* All comments to ADM jr. email: alex,mmiris.ab.umd.edu
%RTFRDR-ERR: unrecognized command:
*
^
%RTFRDR-ERR: unrecognized command:
* All
^^^
%RTFRDR-ERR: unrecognized command:
* All comments
^^^^^^^^
%RTFRDR-ERR: unrecognized command:
* All comments to
^^
%RTFRDR-ERR: unrecognized command:
* All comments to ADM
^^^
%RTFRDR-ERR: unrecognized command:
* All comments to ADM jr.
^^^
%RTFRDR-ERR: unrecognized command:
* All comments to ADM jr. email:
^^^^^
%RTFRDR-ERR: unrecognized command:
* All comments to ADM jr. email:
^
%RTFRDR-ERR: unrecognized command:
* All comments to ADM jr. email: alex,mmiris.ab.umd.edu
^^^^^^^^^^^^^^^^^^^^^^
RTFRDR>* telephone: 410-706-7442
%RTFRDR-ERR: unrecognized command:
*
^
%RTFRDR-ERR: unrecognized command:
* telephone:
^^^^^^^^^
%RTFRDR-ERR: unrecognized command:
* telephone:
^
%RTFRDR-ERR: unrecognized command:
* telephone: 410-706-7442
^^^^^^^^^^^^
RTFRDR>*
%RTFRDR-ERR: unrecognized command:
*
^
RTFRDR>27 1
%RTFRDR-ERR: unrecognized command:
27
^^
%RTFRDR-ERR: unrecognized command:
27 1
^
RTFRDR>
RTFRDR>!
RTFRDR>! references
RTFRDR>!
RTFRDR>!PROTEINS
RTFRDR>!
RTFRDR>!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr.,
R.L.;
RTFRDR>!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha,
S.;
RTFRDR>!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.;
Mattos,
RTFRDR>!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
RTFRDR>!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub,
J.;
RTFRDR>!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.
All-atom
RTFRDR>!empirical potential for molecular modeling and dynamics Studies of
RTFRDR>!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
RTFRDR>!
RTFRDR>!PHOSPHOTYROSINE
RTFRDR>!
RTFRDR>!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C.
RTFRDR>!Structural Characterization of the Phosphotyrosine Binding Region
of a
RTFRDR>!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular
Dynamics
RTFRDR>!Simulation and Chemical Shift Calculations. Journal of the
American
RTFRDR>!Chemical Society, 1996, 118: 11265-11277.
RTFRDR>!
RTFRDR>!IONS (see lipid and nucleic acid topology and parameter files for
RTFRDR>!additional ions
RTFRDR>!
RTFRDR>!ZINC
RTFRDR>!
RTFRDR>!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
RTFRDR>!Solution: A Simple but Accurate Nonbonded Representation,
PROTEINS:
RTFRDR>!Structure, Function, and Genetics 23:12-31 (1995)
RTFRDR>!
RTFRDR>!references
RTFRDR>!
RTFRDR>!LIPIDS
RTFRDR>!
RTFRDR>!Feller, S. and MacKerell, Jr., A.D. manuscript in preparation
RTFRDR>!
RTFRDR>!and
RTFRDR>!
RTFRDR>!Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus,
M.
RTFRDR>!Empirical Potential Energy Function for Phospholipids: Criteria
for
RTFRDR>!Parameter Optimization and Applications, in "Biological Membranes:
A
RTFRDR>!Molecular Perspective from Computation and Experiment," K.M. Merz
and
RTFRDR>!B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81.
RTFRDR>!
RTFRDR>!new ALKANES
RTFRDR>!
RTFRDR>!Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical
Approach
RTFRDR>!for the Optimization of Lennard-Jones Parameters. Journal of
RTFRDR>!Computational Chemistry, 1998, 19: 334-338.
RTFRDR>!
RTFRDR>!ALKENES
RTFRDR>!
RTFRDR>!Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D.,
RTFRDR>!Molecular Dynamics Simulation of Unsaturated Lipids at Low
Hydration:
RTFRDR>!Parameterization and Comparison with Diffraction Studies.
Biophysical
RTFRDR>!Journal, 73:2269-2279, 1997.
RTFRDR>!
RTFRDR>!new PHOSPHATE
RTFRDR>!
RTFRDR>!MacKerell, Jr., A.D. Influence of Water and Sodium on the
Energetics
RTFRDR>!of Dimethylphosphate and its Implications For DNA Structure,
Journal
RTFRDR>!de Chimie Physique, 1997, 94: 1436-1447.
RTFRDR>!
RTFRDR>!IONS
RTFRDR>!
RTFRDR>!all ions from Roux and coworkers
RTFRDR>!
RTFRDR>!Sodium
RTFRDR>!
RTFRDR>!Beglov, D. and Roux, B., Finite Representation of an Infinite
RTFRDR>!Bulk System: Solvent Boundary Potential for Computer Simulations,
RTFRDR>!Journal of Chemical Physics, 1994, 100: 9050-9063
RTFRDR>!
RTFRDR>
RTFRDR>MASS 1 H 1.00800 H ! polar H
%ATOM-MASS=-ERR: real number expected:
MASS 1 H
^
%RTFRDR-ERR: unrecognized command:
MASS 1 H 1.00800
^^^^^^^
%RTFRDR-ERR: unrecognized command:
MASS 1 H 1.00800 H
^
RTFRDR>MASS 2 HC 1.00800 H ! N-ter H
%ATOM-MASS=-ERR: real number expected:
MASS 2 HC
^^
%RTFRDR-ERR: unrecognized command:
MASS 2 HC 1.00800
^^^^^^^
%RTFRDR-ERR: unrecognized command:
MASS 2 HC 1.00800 H
^
RTFRDR>MASS 3 HA 1.00800 H ! nonpolar H
%ATOM-MASS=-ERR: real number expected:
MASS 3 HA
^^
%RTFRDR-ERR: unrecognized command:
MASS 3 HA 1.00800
^^^^^^^
%RTFRDR-ERR: unrecognized command:
MASS 3 HA 1.00800 H
^
RTFRDR>MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
%ATOM-MASS=-ERR: real number expected:
MASS 4 HT
^^
%RTFRDR-ERR: unrecognized command:
MASS 4 HT 1.00800
^^^^^^^
%RTFRDR-ERR: unrecognized command:
MASS 4 HT 1.00800 H
^
RTFRDR>MASS 5 HP 1.00800 H ! aromatic H
%ATOM-MASS=-ERR: real number expected:
MASS 5 HP
^^
%RTFRDR-ERR: unrecognized command:
MASS 5 HP 1.00800
^^^^^^^
%RTFRDR-ERR: unrecognized command:
MASS 5 HP 1.00800 H
^
RTFRDR>MASS 6 HB 1.00800 H ! backbone H
%ATOM-MASS=-ERR: real number expected:
MASS 6 HB
^^
%RTFRDR-ERR: unrecognized command:
MASS 6 HB 1.00800
^^^^^^^
%RTFRDR-ERR: unrecognized command:
MASS 6 HB 1.00800 H
^
RTFRDR>MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2
%ATOM-MASS=-ERR: real number expected:
MASS 7 HR1
^^^
%RTFRDR-ERR: unrecognized command:
MASS 7 HR1 1.00800
^^^^^^^
%RTFRDR-ERR: unrecognized command:
MASS 7 HR1 1.00800 H
^
RTFRDR>MASS 8 HR2 1.00800 H ! (+) his HE1
%ATOM-MASS=-ERR: real number expected:
MASS 8 HR2
^^^
%RTFRDR-ERR: unrecognized command:
MASS 8 HR2 1.00800
^^^^^^^
%PARSER-ERR: Too many parsing errors --> termination
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BOMLEV= 0 reached. Program execution will be terminated.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Subroutine DIE called . Terminating
Yours sincerely
Rajbinder Kaur Virk
--
*With regards*
*Rajbinder Kaur Virk*
*Research Scholar *
*Department of Biophysics*
*Panjab University *
*Chandigarh-160014*
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