Re: [gmx-users] add atoms to gmx saxs

On 2/21/18 3:33 PM, Servis, Michael wrote: Is there a good way to add new atoms with their Cromer-Mann coefficients for use with gmx saxs? Thanks! You can add entries to sfactor.dat (found in $GMXLIB). -Justin -- == Justin A. Lemkul, Ph.D.

Re: [gmx-users] Inconsistent Shifts

Iman, Updating to the latest version is always a good idea. However, the warning you have gotten doesn't actually effect any results you obtain from running the simulation. You simulation still gets completed, doesn't it? So you can actually ignore it then, and update to the latest versions of

[gmx-users] add atoms to gmx saxs

Is there a good way to add new atoms with their Cromer-Mann coefficients for use with gmx saxs? Thanks! Michael -- 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

Re: [gmx-users] Why "do_dssp" gives one more residue?

On 2/21/18 1:04 PM, ZHANG Cheng wrote: Dear Justin, Thank you. But it does not make sense to me. Do you know if separator line is always all the ~ ? If the separator line is following the 214th residue, the 215th residue should be the separator line, but why the 215th residue contains the

[gmx-users] installation problem

Hi there, I want to install gromacs-5.0.7 with this installation guide, tar xfz gromacs-5.0.7.tar.gz cd gromacs-5.0.7 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC after running all of

Re: [gmx-users] Why "do_dssp" gives one more residue?

Dear Justin, Thank you. But it does not make sense to me. Do you know if separator line is always all the ~ ? If the separator line is following the 214th residue, the 215th residue should be the separator line, but why the 215th residue contains the secondary structure? You can find my files

Re: [gmx-users] Why "do_dssp" gives one more residue?

On 2/21/18 12:34 PM, ZHANG Cheng wrote: Dear Qinghua, Yes, exactly! But the numbering is: 1-214: first chain 215-442: second chain However, for the secondary structure codes: 214th:

Re: [gmx-users] Why "do_dssp" gives one more residue?

Dear Qinghua, Yes, exactly! But the numbering is: 1-214: first chain 215-442: second chain However, for the secondary structure codes: 214th:

Re: [gmx-users] Why "do_dssp" gives one more residue?

Hello, Maybe you have two chains in your system, then there should be one for chain separator. Best, Qinghua On 02/21/2018 06:20 PM, ZHANG Cheng wrote: Dear Gromacs, My protein only has 442 residues. After running gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map

[gmx-users] Why "do_dssp" gives one more residue?

Dear Gromacs, My protein only has 442 residues. After running gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to

Re: [gmx-users] ZNO-HSA (Human Serum albumin) Interaction

Hard to tell from your descriptions. Things to consider: 1) Is the force-field for the ZnO particle realistic (have you validated it or have evidence that it is accurate) 2) If the ZnO particle has a net charge and you are running PME you are going to need to neutralize the system such that it

Re: [gmx-users] Calculate RDF within a certain distance from atom

Hi, I think the selection keywords in the manual are helpful: http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html#selection-examples /Mahsa On Tue, Feb 20, 2018 at 5:53 PM, Dilip H N wrote: > Hello, > How to get RDF within a certain distance..??

Re: [gmx-users] how to calculate protein-ligand interaction energy?

Hi Mark, What I'm doing, is unbiased-molecular dynamics simulation. in similar to the following reference that the interaction energy is calculated. https://www.ncbi.nlm.nih.gov/pubmed/21545110 I think the calculation of interaction energy is favourable for these type of studies, only I'm not

Re: [gmx-users] How to obtain TIP4P/? water model topology file

Hi Mark, Thanks a lot for the suggestion. I will try it. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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

Re: [gmx-users] how to calculate protein-ligand interaction energy?

Hi, You should probably follow the working a paper or tutorial that computes such a thing. But it probably won't give you a meaningful result, because I am not aware of a force field that is parameterized so that such a is meaningful. Computing free energy of binding would be meaningful. Mark

[gmx-users] how to calculate protein-ligand interaction energy?

Dear Gromacs Users, I want to calculate protein-ligand interaction energy. as far as I figured out Its summation of these six options in gmx-energy: LJ-14: Ligand-Ligand Coul-14: Ligand-Ligand Coul-SR: Ligand-rest LJ-SR: Ligand-rest Coul-LR: Ligand-rest LJ-LR: Ligand-rest I doubt about My

Re: [gmx-users] Calculate RDF within a certain distance from atom

Justin already properly addressed the original post, so I'll just add a few comments about the last message: > I have the RDF between Calpha-Ow, and it is showing a slight hump/peak around 0.47nm. So you've managed to calculate it then as Justin suggested? FYI the RDF minimum occurs at a larger

[gmx-users] ZNO-HSA (Human Serum albumin) Interaction

Dear Gromacs Users; I am studying the toxicity effect of ZnO nanoparticle (with a partial charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on the Albumin structure by Gromacs. For MD simulation the nanoparticle was placed at a distance of 1nm of protein, after running