ParmEd protocols

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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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  • person_outline Jason Swails <>

ParmEd in pipeline

2015
PMCID: 4639397
PMID: 26245379
DOI: 10.1038/nature14886

[…] parameter set for protein molecules, lipid molecules, and salt ions, and the charmm tip3p model for water; protein parameters incorporated cmap terms-. these parameters were assigned using the parmed implementation of chamber, provided with ambertools14. ligand parameters were based on the results from the charmm paramchem web server, version 0.9.7.164, and incorporated specific […]


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ParmEd in publications

 (19)
PMCID: 5935666
PMID: 29728618
DOI: 10.1038/s41467-018-04176-x

[…] 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 […]

PMCID: 5649594
PMID: 28875361
DOI: 10.1007/s10822-017-0059-9

[…] 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 […]

PMCID: 5570944
PMID: 28839177
DOI: 10.1038/s41598-017-09229-7

[…] 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 […]

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

[…] and those for phase 2 are described in table .table 1 table 2 apregnant women will not be eligible for initial recruitment into the study. women who become pregnant during the study will complete a parmed-x for pregnancy with their physician to identify any contraindications to yoga and will be able to continue participation , apregnant women will not be eligible for initial recruitment […]

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

[…] 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 […]


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