We solved the RNA structure using NMR. we would like to refine the structure using Gromacs or amber. does anyone know that how to convert the xplor distance restraints/dihedral to Gromacs (disre.itp) or amber format for RNA ?
Thanking you.
You may find this helpful:
NAME
xplor2gmx - Convert XPLOR distance restraints to Gromacs format
SYNOPSIS
xplor2gmx (residue offset) input.pdb
DESCRIPTION
xplor2gmx reads an XPLOR input file with distance restraint data as
sometimes is found in the pdb database (http://www.pdb.org ). From this
input file dihedral restrints should be removed, such that only
distance restraints are left. The script can handle ambiguous
restraints. It converts the distance restraints to GROMACS format.
A restraints file (.dat) should be provided on STDIN, and a suitable
output file (.itp) is sent to STDOUT.
EXAMPLES
xplor2gmx.pl 33 conf.pdb < restraints.dat > disre.itp
OPTIONS
xplor2gmx requires two command line options: first, the residue offset
(integer); second, the .pdb filename. The pdb file must have correct
atom numbers.
Reference:
http://manpages.ubuntu.com/manpages/utopic/man1/xplor2gmx.1.html
Dear John Anyam,
Thanks for your reply. i will try to work on it :-)
Looks like this command works only works for protein not for RNA/DNA.
it is showing following error :
Can not open atom-name translation table /usr/local/gromacs-5.0.4/share/gromacs/gromacs/top/atom_nom.tbl
Then i checked the atom_nom.tbl
vi atom_nom.tbl
# Correlation of hydrogen atom naming systems, including diastereotopic
# protons. The original version of this table was created by Charles
# Hoogstraten.
#
# BMRB = System in use at BioMagResBank (IUPAC/IUB Biochemistry 9, 3471-3479
# [1970]).
# SC = Stereochemical designations
# UCSF = Mardigras-type software (peptide protonated with newhyd utility).
# XPLOR = Peptide protonated with XPLOR 3.1. Atom nomenclature is derived
# from the X-PLOR topology file topallhdg.pro.
# MSI = Artificial peptide created with InsightII. For the side chain
# protons attached to nitrogen in ASN, GLN, and ARG, the atom
# nomenclature does not reflect the potential stereoisomerism of the
# planar amide and guanidinium groups. The correlation with Z and E
# nomenclature listed here simply reflects the state of the artificial
# peptide generated as an example. The CG1 and CG2 atoms for VAL in a
# peptide generated by InsightII are not labeled according to IUPAC
# rules, while the CD1 and CD2 atoms for LEU are.
"atom_nom.tbl" [readonly] 407L, 8016C
I followed the below instructions to install Gromacs-5.1.4 after patching up with plumed. and then ran gromacs-plumed simulations end up with following errors. I didnt see any errors, while...
07 August 2017 8,661 0 View
I finished docking based on NMR data and MD simulations using Gromacs . I would like to know that What kind of data should be provide from simulations to explain or confirm the multiple...
31 December 2013 8,131 1 View
We did the Gromacs MD simulation for the protein complex , the complex is stable during 15 ns Simulation. We would like to plot the interface area plot for the protein complex along the entire...
11 December 2013 10,119 6 View
Could anyone provide references or protocols to measure the binding affinity by using fluorescent ligand with protein? Ligand shows fluorescence excitation/emission: 270/340 nm.
10 November 2013 3,030 10 View
I would like to setup unrestrained MD simulations on gromacs for protein-protein complex . The protein complex was calculated by HADDOCK by using NMR Chemical shift restraints? Could you please...
02 March 2013 8,501 2 View
I would like to calculate the number of water molecules replaced before and after complex formation on the binding surface? How we can do this? Any suggestions?
11 December 2012 4,269 8 View
I am new to MD simulation for Protein - protein complex , sorry for asking some basic questions ! 1. What Kind of information it will provide if I do MD simulation for protein complex after...
09 October 2012 9,944 2 View
I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?
11 August 2024 3,115 1 View
Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...
11 August 2024 7,082 3 View
"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....
10 August 2024 8,621 1 View
Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...
10 August 2024 8,992 0 View
I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...
10 August 2024 8,539 5 View
Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...
08 August 2024 6,134 12 View
I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...
08 August 2024 9,882 2 View
I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.
07 August 2024 6,622 1 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
There are a huge number of methods for studying objects in space, according to the senses (and not only). Mechanical, thermal, optical, acoustic, electrical, magnetic, based on particle beams,...
06 August 2024 7,102 0 View