[gmx-users] Energy minimization for Inositol pyrophosphate

ashish bihani ashish.bihani at outlook.com
Wed Feb 25 07:16:46 CET 2015

I have understood my mistakes that I reported in previous queries of this string. now, I am proceeding more systematically.

I have generated ff parameters for Inositol Pyrophosphate with the help of PRODRG server (as mentioned in the tutorials) as a residue and added it to aminoacids.rtp. I was able to reformat atoms, bonds, bond angles, dihedrals and impropers by imitating the format of the definitions of other residues. But I am not able to find a format for [ pairs ] which I believe is important for my experiment. 
Particular pairs defined in ffnonbonded.itp file of gromos54A7 do not have codes unlike dihedrals. If I have two columns for individual atoms (e.g. O35 tab P15 tab ?) involved in the interaction, how do I point the program to corresponding c6 and c12 values in ffnonbonded.itp?

Secondly, the parameter file generated by PRODRG does not contain all the possible dihedral in Inositokl Pyrophosphate. Are those interactions ignored because of some criteria or should I add them manually?

From: ashish.bihani at outlook.com
To: gmx-users at gromacs.org
Subject: RE: Energy minimization for Inositol pyrophosphate
Date: Fri, 30 Jan 2015 12:25:43 +0530


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

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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