Im trying to run x.pdb file but when select force field it give Error(Residue not found).already tried different force field but keep same error. what can to do to solve this error?
See the pdb file of input structures and specifically the atom types. You have to decide the appropriate force field based on the pdb file or vice versa. What I presume from the information you have provided is the force field you are trying to use is not compatible or could not recognize the atom types. Also see whether your pdb contains only standard amino acids, if contains nonstandard residues then you have to provide the parameters for these nonstandard residues additionally in the force field used.
If the problem appear in this point probably you don't parametrized the forcefield for not default molecule. So
you need do it. Open .rtp file and put parameters to molecule.
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Dear Justin Lemkul
I read those links you give me about my question but its show confused for me can give some example to solve.
best regards
Consult the existing examples in the .rtp file for your force field. Entering the information is a simple matter - atom types, charges, and connectivity. Deriving the parameters you need for some non-standard residue is another matter; that's the hard part.
Dear osman,
Really what Justin has suggested is worth to note especially regarding non-standard residues. Unless you provide the MOST correct parameters for non-standard residues, the Gromacs simulation may not work to its capabilities. You will find Justin's suggestions of great help and keep trying.
Thanks Justin and appriciate your attentions to nearly all queries.
Regards
Rajesh Patil
Thank you so much i will try to follow examples then see what is the issue.
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