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"Atomtype O not found" error in gromacs 5.1.1

md simulation gromacs written 11 days ago by SS • 0

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416

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GROMACS fatal error

md simulation gromacs written 10 months ago by amitunited0532 • 10

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347

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Need to know the importance of prediction

md simulation structure prediction written 13 months ago by sakshisingh.bioinfo • 30 • updated 13 months ago by WouterDeCoster ♦ 38k

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724

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MD simulation using YASARA

md simulation written 2.1 years ago by sakshisingh.bioinfo • 30

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898

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how much time should i run MD simulation to check stability of predicted structure?

md simulation written 2.6 years ago by rajeshkumar_vinod • 30

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670

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Lipid Nanoparticle Interaction- MD Simulation

lipid nanoparticle interaction md simulation written 2.7 years ago by Zaved Hazarika • 0

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786

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Unexpected Molecular Dynamics results

md simulation written 3.6 years ago by f.dehghanian68 • 30

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Recent Replies

A: Trouble with BLAST using Biopython by tpaisie • 70
Updated and still doing the same exacting thing.
A: Why do we need a .fai file and a .dict file of the reference during alignment an by Pierre Lindenbaum ♦ 118k
index for bwa-mem : burrow-wheeler transform index used to map the reads. index fai : used by th...
A: ChIP-seq Peak Calling/File Format by Friederike ♦ 3.6k
I don't think you downloaded the peaks, as ATpoint mentioned, these are probably bed files of rea...
C: Writing a bash loop to convert sams to bams by RamRS ♦ 21k
You don't need the `basename` sub-shell call, you can simply use `${file/%sam/bam}`. Bash has pow...
C: Specific Antibodies for ChiP-Seq assay by Friederike ♦ 3.6k
It seems that you will need to read up on the basics of antibody generation, e.g. [here](https://...
C: Whole Genome Assembly with Large Deletions by jb • 0
This looks like it could be extremely useful. Thank you for the recommendation!
C: Whole Genome Assembly with Large Deletions by jb • 0
This makes a lot more sense now. Thank you for the reply!
A: Writing a bash loop to convert sams to bams by st.ph.n • 2.4k
for file in *.sam; do samtools view -S -b $file > "`basename $file .sam`.bam" ...
C: Writing a bash loop to convert sams to bams by RamRS ♦ 21k
This is a pure shell question. For starters, you don't need `files=$(ls); for f in $files`, you c...
C: Whole genome alignments by oussriradnane • 0
my strains have 4 chromosomes, can I compare chrormosome by chromosome or gather all genes (conca...
C: how to interpret hisat2 result by WouterDeCoster ♦ 38k
The summary mentions both pairs and individual reads.
C: Why do we need a .fai file and a .dict file of the reference during alignment an by RamRS ♦ 21k
AFAIK only the GATK and Picard tools need the `dict` files. You're right, `fai` and `dict` are bo...

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