Can someone help me with this GROMACS energy minimization fatal error?

1) I use steepest to minimize energy, .mdp as follows, title = bovin cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE constraints...

05 June 2013 2,375 2 View

Free energy of solvation about peptide

I have some peptides and want to compare their free energy of solvation to see if any difference exists. If I calculate the free energy using GROMACS, and use g_bar -f md*.xvg -o -oi -oh program,...

04 May 2013 7,224 0 View

Can the RMSF of completely different proteins be used as a measure of these proteins flexibility?

After simulation we get the RMSF for each protein. Can we use the RMSF to compare these proteins? In most papers, wild type and mutation types are compared. Could we tell which proteins are more...

08 September 2012 5,820 4 View

Can anyone tell me any tools/software or web server to calculate package density of proteins or peptides?

I have some peptides and want to see the package density of them, but I don't know how to calculate these. I searched online, but did not find any proper method. Can anyone give me any suggestion?...

04 May 2012 274 1 View

Are there any software or tools to calculate protein or pepetide's packing density?

I have some peptides and want to see if any different characters between them. Could you give me some suggestions?

01 February 2012 912 0 View

Hydrogen bond calculation

I have some peptides and want to see how many hydrogen bonds each could form. Please recommend software or web sever I can use, Thank you very much!

01 February 2012 3,143 9 View

What's the way to evaluate a protein's thermodynamic stability ?

method or software? Thank you very much!

11 December 2011 3,841 0 View

Burial of non-polar surface area

Hi, has anyone recommend a program for calculating protein's burial of non-polar surface area?

10 November 2011 1,364 3 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