Need an experts advice to validate our parameterization using non-native sugar molecule?

Dear All, Recently, we have used cgenff Parachem web server "https://cgenff.paramchem.org/" to generate parameters for glucosylated aspartyl residue that exist in high energy non-native sugar (x)...

02 March 2018 4,949 1 View

How to solve the "no default type errors" in GROMACS-5.0.7 using CHARMM36.ff ?

I am trying to run simulation of a glucosylated residue which covalently interact with aspartate. During validation of topology and preparation of energy minimization (EM) step (grompp) I am...

01 February 2018 9,702 8 View

Does anybody knows how to convert Charmm 22 DIHR values to amber format?

Dear All, We are working on parametrization of x non-standard (NR) residue using Charmm22, GLYCAM 06 (amber format) and GAFF force fields. Among these, we can able to parametrize them...

09 October 2017 8,727 3 View

What is a method for understanding the molecular mechanism of protein X?

In a case where we carried out a genetic Screening of genes that involved in the stress response in E. coli. From this screen we identified a gene that encodes a 50 kDa flexible protein (Protein...

10 November 2016 7,394 4 View

How to generate a topology file for structures that has covalent bond (link between RESIDUE and Ligand) in GROMACS?

07 August 2016 6,805 7 View

Does any one used B-D-GLUCOSE .rtp file for amber99sb.ff / GLYCAM ?

07 August 2016 794 0 View

How to write a DOPE score for selected region of optimized atoms along with whole model in modeller?

Dear All, I have tried to generates models for single point mutation along withown optimization and refinement criteria on the selected region of atomsaround the mutated residue which works fine...

06 July 2016 4,281 2 View

How to optimize & refine the conformation of the mutant side chain along with the backbone by using modeller (mutate_model.py ) ?

05 June 2016 2,722 4 View

How to generate a model with double mutant & combination of mutants by using mutate_model.py ?

Dear All, I hope you all know that default mutate_model.py script works only for single mutation but I want to make it for double and combination of mutation and I beleive this would be possible...

05 June 2016 3,316 1 View

I would like to know Is their any bioinformtics stand alone tool for predict the protein stability changes upon mutation ?

Hi All, I am looking for the best bionformatics tool to predict the protein stability changes upon mutation and I found that there is many tools avail for the same here...

04 May 2016 3,786 6 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