Re: [gmx-users] KALP15 in DPPC

On 1/15/18 6:18 AM, negar habibzadeh wrote: tnx Justin . now I am doing Simulation of *5 *Peptide in DOPC Lipids I am following your tutorial, in NVT equilibration step I created index file , with program make_ndx (gmx make_ndx -f em.gro -o index.ndx) : 0 System : 30700 atoms

Re: [gmx-users] force field parameters clashing

On 1/15/18 9:45 AM, Harsha Ravishankar wrote: Dear All, I am a beginner with Gromacs and simulations and I want to simulate a membrane and protein complex with the membrane comprising of 5 different lipid molecules. The membrane was generated with Charmm-GUI and the appropriate Gromacs

Re: [gmx-users] KALP15 in DPPC

tnx so much i got nvt.tpr and now i want to run it but i am getting this error : Fatal error: Too many LINCS warnings (5258) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

Hello, I have finally resolved my problem thank to Justin . Bye -- Message: 2 Date: Sun, 14 Jan 2018 17:36:21 -0500 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem fpr building a peptide with two modified

[gmx-users] Fwd: two very basic questions on new parameters for gromos forcefield

Dear all, I have been working with some new molecules and some new bonded parameteres that I added to the gromos 54a7 files in gromacs according to the manual and so on, and all the results of MD simulations are in perfect agreement with the experimental results. However, I've just been

[gmx-users] force field parameters clashing

Dear All, I am a beginner with Gromacs and simulations and I want to simulate a membrane and protein complex with the membrane comprising of 5 different lipid molecules. The membrane was generated with Charmm-GUI and the appropriate Gromacs parameters for the different lipids were also obtained.

[gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

Hi Gromacs folks, I have a modified amino acid which has all the parameters set. However, the last error is the "cmap torsion between atoms xxx" and it would't go away. Basically the cmap contains atoms of C-N-CA-C-N from three residues, where the CA is my newly modified residue. THe only

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

On 1/15/18 2:56 PM, MD wrote: updated, I figured it is because my N and CA have different type names than charmm, which is weird cause I used CHARMM GUI to get the itp files for the modified amino acid. Would it be an easy fix if I manually change those two atom names or I should go a

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

On 1/15/18 3:06 PM, MD wrote: I wonder if there is a way I can create my own cmap for those modified type names and incorporate the cmap to the cmap.itp? That will end up being far more work than a proper parametrization of the side chain while leaving the backbone alone at standard atom

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

>> Would you be willing to share the exact sequence of events, commands, etc. >> that worked? OK, Consider that the Atosiban cyclic peptide (https://fr.wikipedia.org/wiki/Atosiban) with 2 custom residues (3-Mercaptopropionyl, MEr) and ethyloxyde TYR (TYO) at Nter. The Mer is bonded to the

[gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute" sasa, as it could not reflect the relative

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

On 1/15/18 12:31 PM, ABEL Stephane wrote: Hello, I have finally resolved my problem thank to Justin . Would you be willing to share the exact sequence of events, commands, etc. that worked? As I mentioned before, these threads often trail off or end unresolved, so while it is nice that

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

updated, I figured it is because my N and CA have different type names than charmm, which is weird cause I used CHARMM GUI to get the itp files for the modified amino acid. Would it be an easy fix if I manually change those two atom names or I should go a different route for the cmap problem?

Re: [gmx-users] Fwd: two very basic questions on new parameters for gromos forcefield

On 1/15/18 9:57 AM, Pedro Deira wrote: Dear all, I have been working with some new molecules and some new bonded parameteres that I added to the gromos 54a7 files in gromacs according to the manual and so on, and all the results of MD simulations are in perfect agreement with the experimental

Re: [gmx-users] KALP15 in DPPC

On 1/15/18 10:56 AM, negar habibzadeh wrote: tnx so much i got nvt.tpr and now i want to run it but i am getting this error : Fatal error: Too many LINCS warnings (5258) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/15/18 3:52 PM, ZHANG Cheng wrote: Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? -output is the group you select for output, -o is the file to which the data are

Re: [gmx-users] force field parameters clashing

On 1/15/18 1:27 PM, Harsha Ravishankar wrote: Hello Justin, Thanks for the reply. I only make use of Charmm GUI to generate the membrane patch, as I need to orient my protein in a particular orientation. However when I made use of the .itp forcefield files in gmx grompp -f ions.mdp -c

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

On 1/15/18 1:50 PM, ZHANG Cheng wrote: Dear Gromacs, This website can give us the Q(SASA), i.e. the fraction of SASA per residue, with values from 0 to 1. https://mathbio.crick.ac.uk/wiki/POPS Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the "absolute"

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

Thank you so much for the guide Justin! The path looks clearer to me now :) Ming On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul wrote: > > > On 1/15/18 2:56 PM, MD wrote: > >> updated, I figured it is because my N and CA have different type names >> than >> charmm, which is

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

I wonder if there is a way I can create my own cmap for those modified type names and incorporate the cmap to the cmap.itp? Thanks, Ming On Mon, Jan 15, 2018 at 2:56 PM, MD wrote: > updated, I figured it is because my N and CA have different type names > than charmm, which is

[gmx-users] Uncorrelated Samples, MBAR free energy calculations.

Dear All, I am getting very low number of uncorrelated samples at endpoint of electrostatics transformation. Anyone is familiar with MBAR pyhton script? Javad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I use the below? What is the difference between "-output" and "-o"? echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu ns -- Original

Re: [gmx-users] force field parameters clashing

Hello Justin, Thanks for the reply. I only make use of Charmm GUI to generate the membrane patch, as I need to orient my protein in a particular orientation. However when I made use of the .itp forcefield files in gmx grompp -f ions.mdp -c solvate.gro -p topol.top -o ions.tpr I get errors stating

Re: [gmx-users] -inter command

A lot of OPs have the tendency to follow-up with private emails and I feel it should stay public so other people might benefit from the information as well. Here is the rest of the conversation regarding this thread. """ Dear Zaved, I'm not aware of any tutorials for Gromacs, and Gromacs does

[gmx-users] Rupture force definition

Dear, all I have one query regarding pulling of si-rNA (having chain-a and chain-b). Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b (diagonally apposite ). I am doing pulling using gromacs with constant velocity rate using Umbrella sampling. after finalization of pulling before

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

I mean it is disconnected after energy minimization, i found out the CO is not connecting with the NH from the +1 amino acid. The structure was intact before the simulation. Ming On Mon, Jan 15, 2018 at 6:23 PM, MD wrote: > Hi another quick question, what do you think could

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

Hi another quick question, what do you think could be the problem if the modified amino acid is not connecting to the +1 amino acid? the [cmap ] in merged.rtp already has the [ cmap ]-C NCA C+N Ming On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul wrote: > >

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

On 1/15/18 6:25 PM, MD wrote: I mean it is disconnected after energy minimization, i found out the CO is not connecting with the NH from the +1 amino acid. The structure was intact before the simulation. That has nothing to do with CMAP, that means you didn't properly define a bond to the

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

Sorry I didn't mean to connect it to the cmap. Yes it is a different question. How do I define a bond to the +1 residue please? It is a side chain modified amino acid (LYS) and the backbone is unchanged. What else do I need to take care to make sure the backbone still connects? Thanks a bunch,

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

On 1/15/18 6:36 PM, MD wrote: Sorry I didn't mean to connect it to the cmap. Yes it is a different question. How do I define a bond to the +1 residue please? It is a side chain modified amino acid (LYS) and the backbone is unchanged. What else do I need to take care to make sure the backbone

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

whooops, never paid attention to the C N+, my bad, thank you Justin :) Ming On Mon, Jan 15, 2018 at 6:39 PM, Justin Lemkul wrote: > > > On 1/15/18 6:36 PM, MD wrote: > >> Sorry I didn't mean to connect it to the cmap. Yes it is a different >> question. How do I define a bond to

[gmx-users] six member ring won't stay flat

Hi Gromacs, I have a modified side chain amino acid and it has a six member ring attached to it. Regarding this ring I had dihedral angles taken care with some 0s and some 180s. However, after minimization my structure looks very strange, the ring is not flat and the dihedral angles in my

Re: [gmx-users] six member ring won't stay flat

On 1/15/18 7:45 PM, MD wrote: Hi Gromacs, I have a modified side chain amino acid and it has a six member ring attached to it. Regarding this ring I had dihedral angles taken care with some 0s and some 180s. However, after minimization my structure looks very strange, the ring is not flat and

[gmx-users] rlist

Hi, I have a user-potential for vdw and coulomb (PME-user). I use vdW and columnb cutoffs= 0.3 and 0.5 respectively. What should be the value of rlist? sorry, I could not find in manual. Best regards -- Gromacs Users mailing list * Please search the archive at

[gmx-users] gaff

hi i want draw topology file for ligand with gaff force field, does gromacs can run this force field? -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Info on umbrella sampling simulation

Dear all, I'm performing an umbrella sampling simulation on an ion pulled from the bulk of a phase1 to the COM of a phase2 (taken as reference) along the z-axys in a biphasic system to calculate the PMF related to the transfer from phase1 to phase2. The box is 3.62 X 3.62 X 7.24 nm and the

Re: [gmx-users] KALP15 in DPPC

tnx Justin . now I am doing Simulation of *5 *Peptide in DOPC Lipids I am following your tutorial, in NVT equilibration step I created index file , with program make_ndx (gmx make_ndx -f em.gro -o index.ndx) : 0 System : 30700 atoms 1 Other : 18744 atoms 2 FR1

Re: [gmx-users] Error while compiling GROMACS 2018

Hello, it seems like you have some manually copied files in your source tree. Please try to remove them and build again. The line you see in the first error message was changed during the recent testing (listed-forces/bonded.cpp) and is causing the error in your local copy

[gmx-users] -inter command

Dear Gromacs Users I have an query regarding gmx pdb2gmx -inter command. Do we use -inter command only for setting the protonation state of charged amino acids in order to perform simulation at different pH? Thank You Regards Zaved Hazarika Research Scholar Dept. Of Molecular Biology and

Re: [gmx-users] -inter command

-inter sets the interactive mode for a bunch of other flags. Most are used for selecting the protonation states of the termini and other residues. It can also be used for interactive SS bridge selection. > "for setting the protonation state of charged amino acids in order to perform simulation at