Does anyone know how to add the chain name into *.gro file?

More Urszula Sylwia Uciechowska-Kaczmarzyk's questions See All

Equlibration errors in GROMACS input file?

I am trying to run equilibration i gromacs 5.0.7 Implicit solvent. My input file is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps =...

11 December 2017 6,620 0 View

Does anyone know a software/application that can be used for preparing a pictures of sequence alignment?

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Any advice on single strand DNA in hairpin conformation?

Does anyone know how to build a ssDNA in hairpin conformation? Does anyone know maybe other software where I could do this? Thank you in advance for any suggestions.

01 February 2015 8,333 6 View

How do I prepapre DNA for NAMD simulations?

Is there any fast way to change the DC on CYT for NAMD?

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Why do I get this error while running psfgen for NAMD?

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How do I prepapre DNA for NAMD simulations?

Is there any fast way to change the DC on CYT for NAMD?

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How can I determine the Hbond occupancy with GROMACS?

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29 October 2014 5,219 13 View

With regards to Gromacs Radius of gyration, how do I analyse the data?

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Is it possible to run RMSD calculations in GROMACS?

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CAS with GROMACS, tutorial availabe?

Does anyone know if there is a tutorial for Computational Alanine Scanning using GROMACS?

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

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fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

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fatal error

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fatal error

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fatal error

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What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

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After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

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Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

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02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

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Justin Lemkul

The .gro file format does not (and cannot) make use of chain identifiers. If you want to use chain identifiers, use PDB format.

Vasiliy Triandafilidi

You can take advantage of such programs like MDAnalysis, which provide you with a powerful Python glue for MD analysis commands. In this link you can learn how to write a PDB file. Just before that use can use command

atoms=u.selectAtoms("all")

atoms.set_name("lalalal some string")

(there is also the same attribute for residues(chains) and etc)

http://code.google.com/p/mdanalysis/wiki/Examples