On 1/30/15 1:55 AM, ashish bihani wrote:
Hello,
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.
Quoting your original message:
"I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the
structure from scratch"
So you have a coordinate file (.gro format is not mandatory). What's the
problem?
-Justin
From: ashish.bih...@outlook.com
To: gmx-us...@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.
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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