[gmx-users] query

Hello every one, I wanna calculate binding energy between protein-ligand complex. I created all the essential files like .xtc, .tpr, .ndx etc and also did download pbsa.mdp file. i'm using the command "g_mmpbsa -f mmpbsa.xtc -s md.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp" to get xvg as

[gmx-users] Inconsistency in user group

Hello GMX users, I want to compute the distance between COM of two residues's side chains by gmx distance option. When I'm specifying the first group from the selection menu as one residue and 2nd group as 2nd residue, I'm getting the following error Inconsistency in user input: Selection

Re: [gmx-users] Inconsistency in user group

Thanks Justin, I followed your answer on the archive while tracing from researchgate which you had replayed to a user and solved the problem successfully. Thanks again. -Amir On Tue, Jan 31, 2017 at 5:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/31/17 7:48 PM,

Re: [gmx-users] Ignoring H-atoms.

Hello Maria, f igoring h-atom command is applied ,,then forcefield will ignore all the added h-atoms What I know about -ignh flag, it does not mean to remove the h-atoms, alternatively means that during the topology generation, the force field is considering the h-atoms as the light atoms and

Re: [gmx-users] Ignoring H-atoms.

? Further more, if the case is likely not to flag the -ignh, what might be the possible consequences? I trust to listen to your precious negotiation. Cheers! Amir On Tue, Feb 7, 2017 at 12:21 AM, Erik Marklund <erik.markl...@kemi.uu.se> wrote: > > > > On 7 Feb 2017, at 08:35

[gmx-users] Force field for Cobalt topology??

Hello gmx users, I'm wondering which would be the best force field to create topology for cobalt. I tried different ff but none of them get the task. I searched the mailing archive too but I couldn't get the way to solve the issue. Dr. Justin has just mentioned (https://www.mail-archive.com/gmx

[gmx-users] water sphere formation

Hello every one, I want to design a simulation system in which water will be used as a sphere. I'm not pretty sure how to design the solvent, as a sphere? Obviously, water will be used as the desired solvent. Best, Amir -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] simulation of ternary complex

I want to simulate ternary complex of protein -DNA -ligand..Is it possible to simulate it combinely? Yeah sure, you can, your order might be protein-DNA-ligand during topology development and gro file format good luck On Tue, Jan 24, 2017 at 2:25 AM, maria khan

[gmx-users] Side chain distance

Hello gmx users, I want to measure the distance between the two residues side chains. I will use the gmx distance to do this. But in the 5.X.X series, I could not find COM (center of mass) as i want to measure the average point for a side chain from where I can measure the distance. Can any one

[gmx-users] Protein and Ligand position restraint

Hello gmx users, I want to conduct md simulation to explore the comparative stability and interaction mechanism of the reference compound (experimentally determined) and the newly screened candidate molecules by virtual screening approach. The gromacs version 5.0.7 is installed on my cluster. I

Re: [gmx-users] deformation in simulation

...@gmail.com> wrote: > Also I dont have traj.xtc file. > > On Thu, Feb 23, 2017 at 1:03 PM, RAHUL SURESH <drrahulsur...@gmail.com> > wrote: > > > what is that compact? > > > > And my protein is still within the system.(BOX) > > > > On

Re: [gmx-users] deformation in simulation

so what did you find? Did you fix the problem? On Wed, Feb 22, 2017 at 11:51 PM, Subashini .K wrote: > Many tutorials suggest to run two equilibrations and then production file. > > > At first, run a restrained equilibrium. > > > Then non-restrained equilibrium followed

Re: [gmx-users] deformation in simulation

means that you didn't produce your simulation run yet? On Thu, Feb 23, 2017 at 12:06 AM, RAHUL SURESH wrote: > I am just doing my production run. I don't get any satisfactory conformer. > > > > On Thu, Feb 23, 2017 at 1:21 PM, Subashini .K >

Re: [gmx-users] deformation in simulation

displayed in vmd > ? > > > On Thu, Feb 23, 2017 at 1:34 PM, Amir Zeb <zebami...@gmail.com> wrote: > > > so what did you find? > > Did you fix the problem? > > > > On Wed, Feb 22, 2017 at 11:51 PM, Subashini .K <subashi...@hotmail.com> > >

Re: [gmx-users] Extending a program

Hello Rahul, Just extend the simulation time in mdp file and repeat the same commands as you done for early 100 ns. Best! On Wed, Feb 22, 2017 at 10:47 PM, RAHUL SURESH wrote: > I have a 100ns simulated file.(md.xtc) I need to extend to another 100 ns. > > do i need

Re: [gmx-users] deformation in simulation

Hey I don't know very well about the problem you have. Did you minimize your system well converged? You may go for conjugate minimization All the best! On Wed, Feb 22, 2017 at 10:53 PM, RAHUL SURESH wrote: > Simulating a protein with 100residues for 200ns doesn't show

Re: [gmx-users] deformation in simulation

hey again converge > at some point but again they do deform. > > > > On Thu, Feb 23, 2017 at 12:26 PM, Amir Zeb <zebami...@gmail.com> wrote: > > > Hey > > I don't know very well about the problem you have. > > Did you minimize your system well converged? &g

Re: [gmx-users] deformation in simulation

sur...@gmail.com> wrote: > using VMD > > On Thu, Feb 23, 2017 at 12:32 PM, Amir Zeb <zebami...@gmail.com> wrote: > > > how do you visualize your system structure? > > > > On Wed, Feb 22, 2017 at 10:58 PM, RAHUL SURESH <drrahulsur...@gmail.com> > > w

Re: [gmx-users] Fwd: residue not found in the database.

Hello Abbas, please suggest me any solution and also tell me can we use any other forcefield or not? You may try Amber family forcefields Residue 97 named ARG of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in the

Re: [gmx-users] REGARDING TOPOLOGY FILE

Hello review the number of atoms in gro file and top file also check that the 2nd line in gro file showing the total number of atoms should be in parallel with all the atoms existed in the gro file this way you may solve the problem good luck On Jan 19, 2017 3:20 PM, "Subashini .K"

Re: [gmx-users] REGARDING TOPOLOGY FILE

gt; The ligand contains only 29 atoms. > > > But, in the top and gro generated by acpype it shows 31 atoms. > > > There lies the problem. > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@m

Re: [gmx-users] REGARDING TOPOLOGY FILE

t; gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Amir Zeb < zebami...@gmail.com> Sent: Thursday, January 19, 2017 12:40 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE can you please recognize that two extra atoms generated by acepype?? On Jan 19,

[gmx-users] Free energy calculations

Hello gmx-users I wanted to compute binding free energy for a protein-ligand complex by gromacs. I sued MM/PBSA approach http://rashmikumari.github.io/g_mmpbsa/ but here the entropic terms could not be computed which is the backbone limitation to restrict the actual free energy determination.

Re: [gmx-users] Protein and Ligand position restraint

Thank you Justin, Got it Amir On Sun, Feb 26, 2017 at 7:52 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/24/17 1:19 AM, Amir Zeb wrote: > >> Hello gmx users, >> >> I want to conduct md simulation to explore the comparative stability and >> inter

Re: [gmx-users] Hbonds analysis

hello go to gro file and find out the atom number from which your concerned residue starats and ends copy the atom numbers inbetween and make a separate selection in your index file for residues and paste therein you will have the residue number once you prompt by putting hbond good luck On Dec

[gmx-users] xtc to dcd conversion

Hi How can I convert xtc file of trajectory to dcd file for dccm analysis? Thanks -- 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/Mailing_Lists * For

Re: [gmx-users] Analaysis

hello mohammad can you please let me know how to install do_dssp on my gromacs 5.0.6 we have downloaded the package but we could not install please help thanks On Dec 11, 2016 11:45 PM, "Justin Lemkul" wrote: > > > On 12/11/16 1:01 AM, ‪Mohammad Roostaie‬ ‪ wrote: > >> >> >>

Re: [gmx-users] Force filed for phosphorylated residues

Hello Mark, Please help me for this issue I want to simulate a protein where ser is phosphorylated. i used charm26 ff but i m getting this error "Atom P in residue SER 4 was not found in rtp entry SER with 11 atoms while sorting atoms". can you please suggest me any possible solution for this

Re: [gmx-users] Force filed for phosphorylated residues

sorry, the ff is charm36 and charm26 is miss typed On Sun, Dec 11, 2016 at 11:15 PM, Amir Zeb <zebami...@gmail.com> wrote: > Hello Surya, > > I want to simulate a protein where ser is phosphorylated. i used charm26 > ff but i m getting this error "Atom P in residue SER

Re: [gmx-users] Force filed for phosphorylated residues

Hello Surya, I want to simulate a protein where ser is phosphorylated. i used charm26 ff but i m getting this error "Atom P in residue SER 4 was not found in rtp entry SER with 11 atoms while sorting atoms". can you please suggest me any possible solution for this issue? Thanks in advance Amir

Re: [gmx-users] Force filed for phosphorylated residues

thanks to all of you for your advice amrir On Mon, Dec 12, 2016 at 4:04 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/12/16 2:15 AM, Amir Zeb wrote: > >> Hello Surya, >> >> I want to simulate a protein where ser is phosphorylated. i used charm26

Re: [gmx-users] How can I calculate Potential Energy of the segment divided by index file?

Hello, According to the best of approach, you may prompt to a list after putting the concerned command and you should select the desired group number like one which you have specified for potential energy in you index file. All the best Amir On Thu, Jan 5, 2017 at 12:58 PM, 大木啓輔

Re: [gmx-users] Free energy calculation of protein and drug

energy. I have used that. > > On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebami...@gmail.com> wrote: > > > hello > > you may use mm/pbsa compiled with gromacs to calculate free energy > > all the best > > > > On Jan 7, 2017 1:27 PM, "tasneem kausar

Re: [gmx-users] Free energy calculation of protein and drug

hello you may use mm/pbsa compiled with gromacs to calculate free energy all the best On Jan 7, 2017 1:27 PM, "tasneem kausar" wrote: > Dear gromacs users > > It is first time I am trying to perform free energy calculation of protein > and drug complex. I am following

Re: [gmx-users] Free energy calculation of protein and drug

Hello Tasneem, Same like you, I'm pretty new to this field too. I don't know enough how to calculate free energy in gromacs. I did only MM/PBSA for binding energy calculations. I'll let you know if i get some thing relevant to your question. All the best. Thanks On Thu, Jan 5, 2017 at 10:28

Re: [gmx-users] Free energy calculation of protein and drug

, "tasneem kausar" <tasneemkausa...@gmail.com> wrote: > Thanks Amir Zeb for your reply > I have read in literature about the FEPsetup to parametrize the complex > file (protein+drug) for simulation. This setup builds files based on amber. > Since I have previously used 54

Re: [gmx-users] Fix the residues

Is TYR and SER are N-terminal and C-terminal residues , respectively? Also, you may compare the corresponding atoms of each residues with same residues present in your system and does not show the mentioned warning. All the best On Fri, Jan 6, 2017 at 10:58 AM, liming_52

Re: [gmx-users] how to compute charged carried by a single residue

> Mark > > On Tue, Dec 20, 2016 at 9:12 PM Amir Zeb <zebami...@gmail.com> wrote: > > > Hello All, > > > > I want to know the total charge carried by a specific residue during or > > after simulation. Please let me know how may I do it? I don't know the &g

[gmx-users] Clustsize error

Hello gmx users, I want gmx clustsize for a protein-ligand complex of 10 ns total run. I'm getting the error like: Fatal error: Lo: 0.0, Mid: 1.0, Hi: 1.0 I don't know how to fix this error? Regards! Amir -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Homology model refinement

Hello, I have created a homology model for a protein, where the seq. identity between the template and target is 40%. The template structure also contains co-factor and an inhibitor in bound form means it is a complex. I'll have to define the ligand binding site in target (homology model) based

Re: [gmx-users] Homology model refinement

el? That'll tell you > whether you need a model with the other parts. > > Mark > > On Thu, 22 Dec 2016 16:51 Amir Zeb <zebami...@gmail.com> wrote: > > > Hello, > > > > I have created a homology model for a protein, where the seq. identity > > between the tem

Re: [gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

Hello, You may follow " http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/ " Everything will go fine Good luck Amir On Wed, Dec 21, 2016 at 8:50 PM, Adarsh V. K. wrote: > Dear all, > > We have a 419 amino acid long protein and planned

Re: [gmx-users] Homology model refinement

superimposed the input protein structure and the snapshot from the last frame, so the rmsd was around 5 angstrom between the two structures. [image: Inline image 1] On Wed, Dec 21, 2016 at 10:27 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Thu, Dec 22, 2016 at 5

Re: [gmx-users] Homology model refinement

Hi Mijiddorj, My target protein size is around 250 residues. It's pretty small and i don't have issue with time. Can you please let me know the actual command line for cluster analysis? Regards! On Thu, Dec 22, 2016 at 12:59 AM, Mijiddorj Batsaikhan < b.mijidd...@gmail.com> wrote: > Hi, > >

[gmx-users] how to compute charged carried by a single residue

Hello All, I want to know the total charge carried by a specific residue during or after simulation. Please let me know how may I do it? I don't know the exact command line Thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] how to compute charged carried by a single residue

alright Mark, Thanks a lot On Tue, Dec 20, 2016 at 3:00 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, Dec 20, 2016 at 9:20 PM Amir Zeb <zebami...@gmail.com> wrote: > > > Thanks Mark for your quick response, > > > > I did

[gmx-users] FAD parameters in CHRAMm36 ff

Hello Folks, I want to simulate a protein where FAD is included as co-factor. I will use CHARMm36 ff but I don't know the residue ID for FAD in this particular forcefield. Anyone please let me know by which name FAD is represented in CHARMm36 ff? Thanks in advance! ~Amir -- Gromacs Users

Re: [gmx-users] FAD parameters in CHRAMm36 ff

nimportant. Most of the necessary > functional groups for FAD are already in CHARMM, just not parametrized > explicitly, so I suspect a CGenFF topology to be of pretty high quality > since the analogy will be strong. > > -Justin > > > >> On Friday, March 31, 2017 9

Re: [gmx-users] Error in free energy calculation

You probably follow umbrella sampling for free energy calculation. If it is so, you may change the position of your drug.itp file in topology file, means that before the protein topology. I hope this might solve your problem. Good luck! Amir On Thu, Mar 16, 2017 at 2:49 AM, Tasneem Kausar

Re: [gmx-users] How to access recent discussion on gmx-user list?

Thanks a lot Das, You really solved my problem. Amir On Mon, Mar 20, 2017 at 3:06 AM, Devashish_Das <dasdevashish...@gmail.com> wrote: > Please use this link: > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ > > On Mon, Mar 20, 2017 at 3:01 PM, Amir Zeb &l

[gmx-users] How to access recent discussion on gmx-user list?

Hello folks, I want to access the updated discussion on gmx-user list but mostly I'm getting into this page while searching for " https://www.mail-archive.com/gmx-users@gromacs.org/index.html;, This page gives me very early discussion like 2013 and data I could find after 2103. Please let me know

Re: [gmx-users] powercut command

please put this command line gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt -o md_1_0.xtc good luck On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya < anshullahariy...@gmail.com> wrote: > My md was running. Suddenly power supply was cuts due to some reason and my > my MD

[gmx-users] Regarding Umbrella sampling

Hello gmx users, I want to calculate binding energy for a protein-ligand complex. Obviously, this is the very first time, I'm handling umbrella sampling, so I faced the following error. WARNING 2 [file pull.mdp, line 65]: Unknown left-hand 'pull_ncoords' in parameter file WARNING 3 [file

Re: [gmx-users] Regarding Umbrella sampling

3/8/17 8:11 PM, Amir Zeb wrote: > >> Hello gmx users, >> >> I want to calculate binding energy for a protein-ligand complex. >> Obviously, >> this is the very first time, I'm handling umbrella sampling, so I faced >> the >> following error. >

Re: [gmx-users] Regarding Umbrella sampling

Thanks Justin, Got it -Amir On Wed, Mar 8, 2017 at 7:08 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/8/17 8:43 PM, Amir Zeb wrote: > >> Thanks Justin, >> >> The current version I'm working on is 5.0.6, and I don't have access to >> update th

Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

Thanks Dr. Justin, Got it -Amir On Fri, Mar 3, 2017 at 5:00 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/3/17 1:49 AM, Amir Zeb wrote: > >> Hi Dr. Justin, >> >> I'm wondering that you have mentioned CHARMm27 is not a valid identifier >> of

Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

Hi Dr. Justin, I'm wondering that you have mentioned CHARMm27 is not a valid identifier of protein forcefield, but we have so many articles already published while using CHARMm27 ff. Can you please let us know how to trace this unsuitability of CHARMm27 especially for protein-ligand simulation?

[gmx-users] membrane-protein simulation

Hello gmx-user I want to simulate a membrane protein with more than one chains like A, B, C etc. I generated the strong_posre.itp file as Justing has kindly explained in his tutorial, and updated the topol.top file by inserting the same lines. I also updated the minim.mdp file by inserting

Re: [gmx-users] membrane-protein simulation

Thanks Justin Got it, it's working. On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/2/17 5:01 AM, Amir Zeb wrote: > >> Hello gmx-user >> >> I want to simulate a membrane protein with more than one chains like A, B, >&g

Re: [gmx-users] MM/PBSA

can you please paste your command line here? we can judge where you are wrong On Aug 9, 2017 12:50 PM, "Kingsley Theras Primus Dass ." < 105726...@gms.tcu.edu.tw> wrote: Hi everyone, I am trying to calculate the binding free energy between protein and ligand by using MM/PBSA. I included all

[gmx-users] trans-membrane protein simulation

Hello gmx-users! I want to simulate a membrane protein, where it sets across the membrane (means that some of the protein's region lays outside the membrane and is water exposed). Obviously, the protein will be experiencing two different environments like membrane and water (heterogeneous

[gmx-users] Distances calculation in umbrella sampling

Hello gmx users, I want to calculate binding free energy for protein-ligand complex by Umbrella sampling in Gromacs. I have extracted each frame's gro file for 500 frames after pulling simulation. Now, I want to calculate the distances between the representative gro files by executing the script

Re: [gmx-users] Distances calculation in umbrella sampling

Solved it, Thanks every one! Amir On Thu, Nov 30, 2017 at 5:06 AM, Justin Lemkul wrote: > > > On 11/30/17 4:04 AM, Rose wrote: > >> Till nowi think the only solution is to use gmx distance for each >> conf.gro files.then use perl script. >> don't forget to delete gmx distance

Re: [gmx-users] Problem with topology generation by Amber 12 ff

this particular HIS also read as HIE by the force filed itself and I should assign them as HIE, because otherwise I will get the same error as mentioned above. Thanks for your consideration! On Mon, Dec 4, 2017 at 6:25 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/4/17 1:45 AM,

[gmx-users] Energy analysis

Hi gromacs users, I want to calculate the energy for comparative analysis of protein with and without metal ion, wherein I would like to determine the influence of metal on protein structural stability. I have used gromacs for simulation. Please suggest me how to do this kind of analysis? Should

Re: [gmx-users] Energy analysis

Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 20 November 2017 at 12:34, Amir Zeb <zebami...@gmail.c

Re: [gmx-users] Energy analysis

and be > highly dependent on the quality of the parameterization of the > metal-protein interactions, for which you would probably need some suitable > experimental data. > > Mark > > On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb <zebami...@gmail.com> wrote: > > > Hi gromacs user

Re: [gmx-users] Distances calculation in umbrella sampling

ed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distance

[gmx-users] Problem with topology generation by Amber 12 ff

Hello gmx users, I have generated topology and coordinate files of ZN metalloprotein by Amber 12 ff. Now I am facing this following issue at grompp run: "ERROR 1 [file topol_Protein_chain_A.itp, line 49741]: No default Improper Dih. types" If I use another ff like Amber99SB- ILDN, there is no

[gmx-users] S-nitrosoylated proteins

Hello folks, Which force field has parameters for S-nitrosoylated cysteine? How may I get it? Thanks! Amir -- 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

[gmx-users] Issue regarding MN+2

Hello dear gromacs users, I want to simulate a protein which has two Mn+2 ions as co-factor. Till the solvation, I could prepare the system, but at neutralization step, grompp gives me this fatal error. Fatal error: Atomtype MN not found My system has this topology for Mn+2: [ moleculetype ] ;

Re: [gmx-users] Issue regarding MN+2

Thanks Dr. Justin. I didn't add this stuff by my own. I have created Mn+2 topology by simple pdb2gmx command. ~Amir On Dec 30, 2017 12:21 AM, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 12/29/17 10:11 AM, Amir Zeb wrote: > >> Hello dear gromacs users,

Re: [gmx-users] Issue regarding MN+2

On 12/29/17 10:39 AM, Amir Zeb wrote: > >> Thanks Dr. Justin. >> >> I didn't add this stuff by my own. >> I have created Mn+2 topology by simple pdb2gmx command. >> > > Someone hacked your files and added it at some point. None of the releases > of the C36

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

ebuild them. > > Mark > > On Mon, Jan 1, 2018 at 5:53 AM Amir Zeb <zebami...@gmail.com> wrote: > > > Hi gmx users, > > > > Wishing you all a very happy new year 2k18. > > > > I have modified a particular Tyr residue to phosphorylated Tyr and >

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

> > 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 Tu

[gmx-users] Error regarding pdb2gmx of modified residue

Hi gmx users, Wishing you all a very happy new year 2k18. I have modified a particular Tyr residue to phosphorylated Tyr and renamed as TP2 per forcefield recognizable name. I have used: gmx pdb2gmx -f xxx.pdb -o xxx.gro -ignh -ter (as full command) C36m ff Gromacs v5.0.6 NH3+ as N-terminus COO-

Re: [gmx-users] Issue regarding MN+2

Thanks Dr. Justin, Let me try. ~Amir On Sat, Dec 30, 2017 at 8:14 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/30/17 12:23 AM, Amir Zeb wrote: > >> Alright Dr. Justin, >> >> Is it kindly possible to get CHARMM-compatible parameters for Mn2+ which

[gmx-users] Residue not found in topology

Hi gromacs users, I want to simulate a protein where one of the lysine residues is modified to acetylated lysine and has been denoted by KAC. I want to simulate it by CharmM 36 ff, but it gave me this error. Program gmx pdb2gmx, VERSION 5.1.4 Source code file:

Re: [gmx-users] Residue not found in topology

ur tool.top file the particular lys molecule residue name you > >> have to modify. Then it will work..Actually grompp can't find the > molecule > >> in the topology. > >> > >> On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, wrote: > >> > >>&g

Re: [gmx-users] Residue not found in topology

not true. The -ignh option ignores H atoms in the input > coordinate file and is useful when there are H atoms with names that do > not agree with what is specified in the .rtp entry for the given > residue. The OP's problem is the opposite: the H are not there but need > to be built. >