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I have a system with parts that the pdb2gmx program... |
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Friday, 09 September 2005 |
I have a system with parts that the pdb2gmx program does not know about, i.e. they have no .rtp entry, but I did make/find an .itp file for it (e.g. for my lipid, cofactor, substrate). What should I do?
The trick is to make a by-pass for the part(s) that pdb2gmx knows nothing about by splitting your input files (.gro or .pdb) into the part that can/should be processed by pdb2gmx (e.g. the protein(s)), and the part that can/should not (e.g. the substrate). Then, into the .top file generated by pdb2gmx you insert a #include statement for the .itp file of your 'other part' and the appropriate entries in the [ molecules ] section, and into the .gro/.pdb file generated by pdb2gmx you re-insert the 'other part' of your input .gro/.pdb file (use editconf to convert .gro to .pdb or back if necessary).
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