[gmx-users] Energy minimization for Inositol pyrophosphate

ashish bihani ashish.bihani at outlook.com
Thu Jan 29 12:24:50 CET 2015

Hello all,
I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc
2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. 
I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you.


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