[gmx-users] to generate phosphotyrosine topology

Dear gromacs users I need to generate topology for my protein-peptide complex which the peptide has 2 phosphotyrosine residues. I used CHARMM36 force field to do that. I n that way, I downloaded this force field from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs and paste it in working

[gmx-users] phosphotyrosine

Dear gmx users I used CHARMM36 ff to generate topology for my complex which has 2 phosphotyrosines. when I issed gmx pdb2gmx command , I faced to this error: Fatal error: Residue 1 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an

[gmx-users] dihedral not created even with ffbonded.itp all set

Hi Gromacs folks, I was trying to combine protein with an arbitrary ligand for simulation. I think there are two routes to go, one is to create the protein.gro and itp with gmx and search the ligand topology on atb or elsewhere, and combine them together manually for further simulation. The other

[gmx-users] Regarding simulation of ions-water system

Hello, I want to simulate Ca2+, CO32- ions in the water system. So these were the following commands i followed: gmx editconf -f abc.gro -box xxx -o def.gro gmx insert-molecules -f def.gro -ci ghi.gro -nmol x -o jkl.gro gmx solvate -cp jkl.gro -cs scp216.gro -o mno.gro gmx pdb2gmx -f mno.gro -o mno

[gmx-users] KALP15 in DPPC: Bilayer out of solvation box

Dear Experts I am currently doing the gromacs tutorial for simulation of membrane protein (KALP15 in DPPC by Justin A. Lemkul). I came across several challenges most of which I could resolve. However, the result after solvation wasn't as expected. That is, a small portion of the DPPC bilayer was o

[gmx-users] Error while installing GROMACS-2018-rc1

I am trying to install the latest GROMACS on Macbook Pro 2017 15-inch (High Sierra) and got the following error message when issuing "make" command during the installation steps. My command for cmake was: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DGMX_USE_OPENCL=O

Re: [gmx-users] Error while installing GROMACS-2018-rc1

Hi, Thanks, we have found and prepared a fix for an issue that looks very similar (https://gerrit.gromacs.org/#/c/7400). Apparently the Mac OpenCL compilation cannot tolerate any extra spaces in the command used to compile the kernels used on the device. You could either compile GROMACS without O

Re: [gmx-users] Regarding simulation of ions-water system

Hi, On Mon, Jan 1, 2018 at 4:40 PM Dilip H N wrote: > Hello, > I want to simulate Ca2+, CO32- ions in the water system. So these were the > following commands i followed: > gmx editconf -f abc.gro -box xxx -o def.gro > gmx insert-molecules -f def.gro -ci ghi.gro -nmol x -o jkl.gro > gmx solvate

Re: [gmx-users] KALP15 in DPPC: Bilayer out of solvation box

Hi, On Tue, Jan 2, 2018 at 3:02 AM Seketoulie Keretsu wrote: > Dear Experts > > I am currently doing the gromacs tutorial for simulation of membrane > protein (KALP15 in DPPC by Justin A. Lemkul). I came across several > challenges most of which I could resolve. However, the result after > solva

Re: [gmx-users] pressure coupling

Hi, On Mon, Jan 1, 2018 at 7:43 AM wrote: > Hello Dr.Lemkul > > Thank you very much for your help and your answer > > my average pessure is 1.5 bar and it fluctuates + and - 295 bar . > > as your guide, I will consider it near to 1 bar. I didn't know what I > should do I thought pressure must co

Re: [gmx-users] Error regarding pdb2gmx of modified residue

Hi, I would rename those atoms exactly as the .tdb file in your force field expects. And if that doesn't work, try deleting them and having pdb2gmx rebuild them. Mark On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb wrote: > Hi gmx users, > > Wishing you all a very happy new year 2k18. > > I have modif

Re: [gmx-users] pressure coupling

Hello Dr.Abraham Thank you very much for your answer Your answer was very clear and I understood it. it was very helpful. Best regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Suppo

Re: [gmx-users] Error regarding pdb2gmx of modified residue

Thanks Mark, Actually, the pdb file which I'm trying to execute for topology generation, has one residue (TYR15) is modified to phosphorylated tyrosine. Once I'm directing to command prompt for selection of termini, N-terminus is fine where it is needed for GLN-2, but the app asking C-terminus for

Re: [gmx-users] Error regarding pdb2gmx of modified residue

Hi, Just as Justin said there, I suspect you missed step 5 of http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field pdb2gmx should also have told you things about how many chains, etc. it found. What was the full output? Mark On Tue, Jan 2, 2018 at 6:52 AM Amir Zeb wro