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 restrain a ligand using GROMACS 2018.2?

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...

06 July 2018 9,844 0 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 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

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 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

MD MOE RMSD

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

07 August 2021 0 0 View

MGL tools

20 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

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

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View