ParmEd statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ParmEd
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Tool usage distribution map

This map represents all the scientific publications referring to ParmEd per scientific context
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Associated diseases

This word cloud represents ParmEd usage per disease context
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Protocols

ParmEd specifications

Information


Unique identifier OMICS_14394
Name ParmEd
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.5.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jason Swails

ParmEd citations

 (26)
library_books

Defining a conformational ensemble that directs activation of PPARγ

2018
Nat Commun
PMCID: 5935666
PMID: 29728618
DOI: 10.1038/s41467-018-04176-x

[…] final unrestrained NTP MD simulation was then run for 200 ps with 2 fs steps. The final restart file from this process was used along with a hydrogen mass repartitioned parameter file (modified using parmed) to run new simulations with new randomized atomic velocities using 4 fs steps at 310 K. Analysis was carried out using CPPTRAJ. All production simulations were carried out using pmemd.cuda or […]

library_books

Effectiveness of SmartMoms, a Novel eHealth Intervention for Management of Gestational Weight Gain: Randomized Controlled Pilot Trial

2017
PMCID: 5617906
PMID: 28903892
DOI: 10.2196/mhealth.8228

[…] deficiency virus, preexisting diabetes (self-report or determined by glycated hemoglobin A1c and/or 75 g oral glucose tolerance test in the first trimester), or with contraindications to exercise (by PARmed-X and American College of Obstetricians and Gynecologists committee opinion #67 []) were excluded. With support of local obstetricians, participants were recruited from brochures placed in vari […]

call_split

Solvation free energies and partition coefficients with the coarse grained and hybrid all atom/coarse grained MARTINI models

2017
J Comput Aided Mol Des
PMCID: 5649594
PMID: 28875361
DOI: 10.1007/s10822-017-0059-9
call_split See protocol

[…] ntechamber and parmcheck programs []. The AA model is thus described by the general Amber force field (GAFF) with AM1-BCC charges [, ].Combining the AA and CG models to a hybrid AA/CG model using the parmed libraries []. A MARTINI AA/CG model consists of the AA model plus the CG model represented as virtual sites (VS) []. The VS sites are mapped on a set of heavy atoms and only interact with solve […]

call_split

Simple MD based model for oxidative folding of peptides and proteins

2017
Sci Rep
PMCID: 5570944
PMID: 28839177
DOI: 10.1038/s41598-017-09229-7
call_split See protocol

[…] he closeness parameter is iteratively adjusted until the desired d is obtained.Three cysteine residues in guanylin were initially assigned to the new CYR type. This new residue type was created using ParmEd program from the AmberTools suite. CYR cysteines are deprotonated and neutral; all parameters of residue type CYR are inherited from the disulfide-bonded type CYX (however, we choose not to cre […]

library_books

A study protocol of a three group randomized feasibility trial of an online yoga intervention for mothers after stillbirth (The Mindful Health Study)

2017
PMCID: 5501104
PMID: 28694991
DOI: 10.1186/s40814-017-0162-7

[…] stretching/toning classes during the study.In the case that a woman becomes pregnant during the study, she will be asked to complete the Physical Activity Readiness Medical Examination for Pregnancy (PARmed-X for Pregnancy), a health screening tool completed with the health care provider to ensure it is safe for women to participate in prenatal exercise. We will also send women a pregnancy safety […]

library_books

Markov modeling reveals novel intracellular modulation of the human TREK 2 selectivity filter

2017
Sci Rep
PMCID: 5428000
PMID: 28377596
DOI: 10.1038/s41598-017-00256-y

[…] vin integrator with a 1.0/ps friction coefficient and a (fully) anisotropic Monte Carlo barostat with a frequency of 25 steps. OpenMM natively reads the prepared forcefield prmtop files. For Gromacs, ParmEd (https://github.com/ParmEd/ParmEd) was used to convert the prmtop topology to the Gromacs “top” format. Gromacs simulations used the velocity-rescaling-with-stochastic-term temperature coupling […]


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