User: dasdevashishdas

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Posts by dasdevashishdas

<prev • 24 results • page 1 of 3 • next >
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How to calculate pH of Protein structure?
... I want to do constant pH MD for an enzyme. For the analysis, I want to know, is there any way to calculate pH of static pdb structure? I have pKa (individual residue) and charge (whole protein). PS: I already did the simulation using, H++ server and Gromacs. ...
ph protein-structure written 8 months ago by dasdevashishdas120 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Pseudo atom in a cavity
... If you already know the atoms of the opening of the cavity, then select and create a new object (obj1) from action menu. Then place a pseudoatom by pseudoatom StartCavity, obj1 ...
written 12 months ago by dasdevashishdas120
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Answer: A: How to set own code to Wizards Menu of Pymol ?
... I know it is nearly 3.5 years! I found the solution. It is "cmd.wizard" wizard distance # launches the distance measurement wizard # set a message cmd.wizard("message", "Hello, I'm a message.") # dimiss the message cmd.wizard() Source: https://pymolwiki.org/index.p ...
written 12 months ago by dasdevashishdas120
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Comment: C: Gromacs-Molecular simulation of a protein and ligand
... Please use https://atb.uq.edu.au for generation of itp file. Post the full error for MKTOP. ...
written 17 months ago by dasdevashishdas120
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Answer: A: RMSF AND ngmx in GROMACS
... 1. **How to check and visualise the box dimension at protein ligand simulation in GROMACS 5.0.4 ?** It depends on which format (PDB, GRO and XTC) you want to use. For visualization: Use VMD ( www.ks.uiuc.edu/Research/vmd , http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD). T ...
written 17 months ago by dasdevashishdas120
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Why single SNP (rsid) belong to more than one Gene?
... Dear all, I wanted to know the reason why there is more than one gene specified for a single RSid (dbsnp)? eg: For **rs3827295** Gene: **LINC01664** and **CECR6** **rs5751876** Gene : **ADORA2A-AS1 + ADORA2A + SPECC1L-ADORA2A** rs35921388 Gene : **GSTTP1 + GSTTP2 + LOC105372959** ...
gene dbsnp snp written 17 months ago by dasdevashishdas120 • updated 17 months ago by WouterDeCoster35k
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Answer: A: Ligand topology with gromacs
... **My first question is: is PRODRG the suitable program for generation of small molecule topologies?** No. please use acpype (webapps.ccpn.ac.uk/acpype/ ) or better use ATB (https://atb.uq.edu.au/ only gromos forcefield). For complete list see: http://www.bevanlab.biochem.vt.edu/Pages/Personal/jus ...
written 17 months ago by dasdevashishdas120
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VQSLOD score different for Full and split (by chromosome) BAM file
... Dear all, I am trying to generate VCF using full and split (by chromosome) BAM files by GATK but after successful completion, there are difference in the VQSLOD score: **For full : VQSLOD=-6.339e-01** **For split : VQSLOD=-1.472e+00** Does this means splitting the BAM is not correct or is it b ...
vcf gatk written 20 months ago by dasdevashishdas120 • updated 18 months ago by Biostar ♦♦ 20
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What are the adapters in illumina platinium genomes?
... Hello All, I want to know the adapters (if present) in the illumina platinium genomes. The website (https://www.illumina.com/platinumgenomes.html) and the paper (http://genome.cshlp.org/content/27/1/157) doesn't talk about it. Also, is there any specific Cutadapt command, we need to pass to get t ...
adapters assembly sequencing written 21 months ago by dasdevashishdas120
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Answer: A: Predicting the 3D structure of a protein
... You have two option: 1. Consider multiple template and go for homology modelling 2. Do Protein threading prediction (http://zhanglab.ccmb.med.umich.edu/I-TASSER/) ...
written 23 months ago by dasdevashishdas120

Latest awards to dasdevashishdas

Popular Question 17 months ago, created a question with more than 1,000 views. For Any free tool for Calculating Gasteiger-Hückel charges for ligands?
Supporter 23 months ago, voted at least 25 times.
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Next Generation Sequencing for Beginners
Student 3.0 years ago, asked a question with at least 3 up-votes. For Any free tool for Calculating Gasteiger-Hückel charges for ligands?
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Using Biopython and BLAST+ to automate de novo viral contig sorting
Scholar 4.0 years ago, created an answer that has been accepted. For A: Using Biopython and BLAST+ to automate de novo viral contig sorting

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