[gmx-users] Energy minimization for Inositol pyrophosphate
ashish.bihani at outlook.com
Fri Jan 30 07:55:47 CET 2015
I understand that .itp is a topology file. But the swissparam pack does not have a .gro file. How do I create solvated.gro ? (which has to be used in grompp)
Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say whether .itp can sustitute the other two.
From: ashish.bihani at outlook.com
To: gmx-users at gromacs.org
Subject: Energy minimization for Inositol pyrophosphate
Date: Thu, 29 Jan 2015 16:53:56 +0530
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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