07 July 2018 0 10K Report

Hi,

I am doing an MD simulation of a protein-ligand complex using GROMACS 2018.2. I want restrain my ligand for that I need to generate a position restraint topology for it. I need a shell script which can create an index group for the ligand that contains only its non-hydrogen atoms. Why I need a shell script, as I am running everything in HPC, I need to write every code inside a shell script which can do my job.

Thanks lot for your time

With regads

Budheswar

More Budheswar Dehury's questions See All
How to compute the numebr of water molecules within a specified distance between two residues of diffrent chains?

Dear All, I want to compute the number of water molecules and their retention period within five angstrom of two catalytci residues belonging to two different chains of a lipid bilayer...

07 August 2019 3,049 14 View

How to solve GMX HELIX Segmentation fault in GROMACS 2018.2?

Dear All, Hi..I am doing analysis of Helix properties using gmx helix program of GROMACS 2018.2 installed in a workstation with CentOS. I have created an index fro my TM and then while I use gmx...

08 September 2018 9,661 0 View

How to solve error in GROMACS?

Dear All, Hi, I have trajectory file of 500 ns of membrane proteins. Though the file is large enough, I have a problem while I use trjconv option it shows the following error... Program: gmx...

07 August 2018 3,408 6 View

How to automate the task of restarting the MD simulation in GROMACS if it stopped due to wall time constraint in HPC?

Hello Everyone, I am trying to run very large systems (membrane protein systems) for longer period of times (say=500 ns). Due to very strict wall time constraint the running MD systems may be...

05 June 2018 8,125 4 View

Which web server performs best in predicting the allergenecity of predicted epitopes?

I have predicted certain group of epitopes. Now I want assess the allegenecity of these predicted epitopes. Dose anybody has any idea which is best tool for allergen prediction... Thanking...

06 July 2015 4,710 2 View

Can someone help me in designing a peptide which can be used as a candidate vaccine from a set of aligned sequences of human viral gene?

11 December 2014 8,890 10 View

What will be the exact keyword to search microarray data of plant-microbe interaction from GEO of NCBI?

Please let me know how to retrieve exact GEO data of plants and infected microbes for comparative analysis of microarray data.

11 December 2013 3,130 1 View

Does anybody have any idea how to find deferentially expressed transcripts in a control and another sample transcript contigs generated from Solid4.0?

I have the transcript contigs of both the samples generated from SOLid4.0. If anybody ahs an idea how to find the up-regulated and down-regulated transcripts (which are .fasta format) using any...

08 September 2013 9,470 3 View

Does anybody knows how to install APBS (APBS-1.4-linux-static-x86_64.tar.gz) in CentOS6.3 version?

I want to calculate binding energy. So I want to install APBS in centos. I have cmake. Please help me out if anybody know how to install APBS step by step in CentOS?

08 September 2013 9,403 0 View

How to install to DSSP for GROMACS?

Step by step Installation of DSSP for GROMACS in CENTOS.

03 April 2013 6,133 4 View

Similar questions and discussions
MD MOE RMSD

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

07 August 2021 0 0 View

MD MOE RMSD

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

07 August 2021 0 0 View

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.

16 June 2021 0 0 View

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.

16 June 2021 0 0 View

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.

16 June 2021 0 0 View

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.

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

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

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

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

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

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

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

Our partners will collect data and use cookies for ad personalization and measurement. Learn how we and our ad partner Google, collect and use data. Agree & close