[gmx-users] energy minimisation error

Dear All, Good morning. I am doing the Protein Ligand complex simulation tutorial from the Gromacs website. I followed the tutorial without any issue. When I want to run the energy minimisation md, i get the error message Fatal error: grid cell cx -2147483648 cy -2147483648 out of range (max 24

[gmx-users] water deletor script error

Dear All, I used Dr. Justin's perl script to delete water from the membrane. It gives an error of illegal division by zero. has anyone experienced it. i looked at the error line it goes like this my $middle_z = $total_z / $nmiddle; I tried a few atom numbers but same error. i wonder if others

[gmx-users] warnings about tip3

Dear All, I m simulating cholesterol membrane with protein embedded in water portion of the upper leaflet of the membrane. I am using Gromacs 2019 built on Windows 10 WSL. My intention is to pull the protein through the membrane from one end to the other into the water part. The membrane was built

[gmx-users] various issues when simulating cholesterol membrane

comes when it reads the cholesterol.itp. So when i will want to parametrise the protein, i will have issues or can i use the same forcefield since the file does have the amino acid parameters also? Kindly suggest what can be the correct way? Thank you Regards Ayesha Fatima -- Gromacs Users mailing

[gmx-users] CHOL still not recognised

Dear Justin, Thank you for your earlier response. I opened the file in vmd and it returned me with a 3 letter residue name and an X identifier for the whole molecule. CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 ATOM 1 C3 CHL X 1 -1.678 2.702 17.328

[gmx-users] gromacs is not recognising opls ff

Dear All, I have come across another issue When i want to use opls itp for cholesterol, it gives me this error " Fatal error: Residue 'OL' not found in residue topology database" It does not take CHOL as the residue name as given below [ atoms ] ; nr type resnr residue atom cgnr

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 180, Issue 46

d md simulation (m mar) >4. Re: make index for protein multiple ligand md simulation > (Soham Sarkar) >5. GMO simulation (Ayesha Fatima) >6. Re: GMO simulation (RAHUL SURESH) > > > --

[gmx-users] GMO simulation

Dear All, I have a glyceryl monooleate 100 molecule assembly. I want to pull a peptide like molecule through it. I have obtained the forcefield files from *Boeckmann, Rainer website.* I followed the Bevan Lab KAlp15 tutorial to build topology of lipids but got stuck as the force field obtained

[gmx-users] Pull code errors

Dear All, I am using Gromax 2019 and running an umbrella sampling for two proteins. It is a simple pulling simulation. It is giving me the following error ERROR 1 [file md_pull.mdp]: When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5

[gmx-users] gromacs compilation in cygwin

-3.3.4/fftw-3.3.4 export CPPFLAGS=-I$/home/ashmer/fftw-3.3.4/fftw-3.3.4/include export LDFLAGS=-L$/home/ashmer/fftw-3.3.4/fftw-3.3.4/lib export Gromacs5=/cygdrive/c export PATH=$Gromacs5/bin:$PATH export LD_LIBRARY_PATH=$Gromacs5/lib:$LD_LIBRARY_PATH ... thank you Ayesha Fatima (UM

[gmx-users] calculating distances in steered dynamics

for the advice. I will follow after I complete this run. Thank you Regards Ayesha Fatima PhD candidate (UM) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support

[gmx-users] error in umbrella sampling tutorial

modifications i get the error ... There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. . Could you guide me through the issue? Thank you Regards Ayesha

[gmx-users] testing gromacs runs

Dear all, I have just installed gromacs 4.6.5 in Cygwin build on Windows 7 platform. I want to test the installation but it keeps giving the error ./gmxtest.pl all ERROR: Can not find executable gmx pdb2gmx in your path. Please source GMXRC and try again. My Gromacs is installed in the C: drive