[gmx-users] Energy minimization for Inositol pyrophosphate

Justin Lemkul jalemkul at vt.edu
Thu Jan 29 13:41:47 CET 2015

On 1/29/15 6:23 AM, ashish bihani wrote:
> 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.

If you have an .itp file, that's a topology.  You don't need to run through 
pdb2gmx again, because the purpose of pdb2gmx is to create a topology.  If file 
formats are unfamiliar to you, refer to Chapter 5 of the manual where all of 
this is covered.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list