Re: [gmx-users] grompp error : Atomtype CAro not found

On 3/3/20 2:47 AM, Atila Petrosian wrote: Dear Justin and Dallas, Thanks for your answers. I am so confused. I am beginner in MD simulation of lipid + small molecule. '' There are far better options for lipids than the old Berger parameters used in the tutorial. I wrote the tutorial in 2008

[gmx-users] grompp error : Atomtype CAro not found

Dear Justin and Dallas, Thanks for your answers. I am so confused. I am beginner in MD simulation of lipid + small molecule. '' There are far better options for lipids than the old Berger parameters used in the tutorial. I wrote the tutorial in 2008 and it reflected a common protocol at the time

Re: [gmx-users] grompp error : Atomtype CAro not found

You need to use the same forcefield. Since you are using ATB to generate the topology for your small molecule, then it stands to reason that you then should use ATB for the lipid molecule. Search ATB, I'm pretty sure the various lipids will already be there, and suspect they will be some that the

Re: [gmx-users] grompp error : Atomtype CAro not found

On 3/2/20 2:40 AM, Atila Petrosian wrote: Hi Dallas, thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB server. My system contains lipid molecules and small molecule. For lipid molecules, Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both of gromos54a7_a

[gmx-users] grompp error : Atomtype CAro not found

Hi Dallas, thanks for your answer. I saw README file in gromos54a7_atb.ff from ATB server. My system contains lipid molecules and small molecule. For lipid molecules, Justine Lemkul suggested to use gromos53a6_lipid.ff. How to use both of gromos54a7_atb.ff and gromos53a6_lipid.ff in topology file

Re: [gmx-users] grompp error : Atomtype CAro not found

Did you read what the ATB told you about the topologies it generates, and what forcefield you have to use? There is a warning posted on the page where you download your topology files that applies directly to this error you have encountered: "*Warning!* This molecule contains non-standard atom ty

[gmx-users] grompp error : Atomtype CAro not found

Hi gromacs users, I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + water molecules) using gromacs 2019. I used ATB for drug molecules and Membrane Protein: KALP15 in DPPC gromacs tutorial method for lipid molecules (based on Justin Lemkul suggestion in my previous post: http

Re: [gmx-users] grompp error : Atomtype HC not found

On 2/14/20 6:09 AM, Atila Petrosian wrote: Dear Justin, Thanks for answer. You said " There is no reason to use this totally obsolete force field (ffgmx.itp)". I used ffgmx.itp, because there was a example.top file in Tieleman's web site: That example is almost as old as I am :) It reproduc

[gmx-users] grompp error : Atomtype HC not found

Dear Justin, Thanks for answer. You said " There is no reason to use this totally obsolete force field (ffgmx.itp)". I used ffgmx.itp, because there was a example.top file in Tieleman's web site: --- ; topology for 1 alm molecule, 128 popc lipids

Re: [gmx-users] grompp error : Atomtype HC not found

On 2/13/20 8:56 AM, Atila Petrosian wrote: Hi gromacs users, I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + water molecules) using gromacs 2019. I used ATB for drug molecules and Tieleman's web site for lipid molecules. ATB uses a custom version of GROMOS96 that use

[gmx-users] grompp error : Atomtype HC not found

Hi gromacs users, I am doing MD simulation of my system (DPPC lipid + 2 drug molecules + water molecules) using gromacs 2019. I used ATB for drug molecules and Tieleman's web site for lipid molecules. --- My topology file is as follows:

Re: [gmx-users] grompp not possible with annealing - Gromacs 2019.1

h.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Mark Abraham Gesendet: Dienstag, 10. September 2019 17:56 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] grompp not possible with annealing - Gromacs 2019.1 Hi, Thanks for the report - but it's probably fixe

Re: [gmx-users] grompp not possible with annealing - Gromacs 2019.1

Hi, Thanks for the report - but it's probably fixed already ( http://manual.gromacs.org/documentation/2019.2/release-notes/2019/2019.2.html#fix-segmentation-fault-when-preparing-simulated-annealing-inputs) so I suggest you get the latest 2019.x release? Mark On Tue, 10 Sep 2019 at 17:15, Tafelme

[gmx-users] grompp not possible with annealing - Gromacs 2019.1

Dear all, I try to use simulation annealing, but unfortunately the grompp - command leads to an error. It is not a known Gromacs error, but it doesn't finish the job and it says: Speicherzugriffsfehler (Speicherabzug geschrieben) (which means something like "Memory Access Error") The only outp

Re: [gmx-users] Grompp not producing tpr files

Great! Thanks!!! -Israel From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Dallas Warren Sent: Monday, June 17, 2019 10:31:43 PM To: GROMACS users Subject: Re: [gmx-users] Grompp not producing tpr files Before you go any further you need to

Re: [gmx-users] Grompp not producing tpr files

ands out is the system's charge. After running > pdb2gmx, the system's overall charge is listed as -1.589 e. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf o

Re: [gmx-users] Grompp not producing tpr files

verall charge is listed as -1.589 e. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Paul Bauer Sent: Thursday, June 13, 2019 8:08:58 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Grompp not producing tpr files Hello, Yes, the last part i

Re: [gmx-users] Grompp not producing tpr files

rael > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Bratin Kumar > Das <177cy500.bra...@nitk.edu.in> > Sent: Wednesday, June 12, 2019 7:00:55 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users]

Re: [gmx-users] Grompp not producing tpr files

Thanks again!! > -Israel > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Bratin > Kumar Das <177cy500.bra...@nitk.edu.in> > Sent: Wednesday, June 12,

Re: [gmx-users] Grompp not producing tpr files

___ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Bratin Kumar Das <177cy500.bra...@nitk.edu.in> Sent: Wednesday, June 12, 2019 7:00:55 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Grompp not producing tpr files Hi Give here the full error On Thu

Re: [gmx-users] Grompp not producing tpr files

Hi Give here the full error On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, wrote: > Hi, > > Was grompp exiting normally, or crashing? Are you looking in the right > place, for a file of the right name? :-) > > Mark > > On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote: > > > Hello users, > > >

Re: [gmx-users] Grompp not producing tpr files

Hi, Was grompp exiting normally, or crashing? Are you looking in the right place, for a file of the right name? :-) Mark On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote: > Hello users, > > > I'm running into problems trying to grompp; I'm using the command > > > gmx grompp -f ions.mdp -c et

[gmx-users] Grompp not producing tpr files

Hello users, I'm running into problems trying to grompp; I'm using the command gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top and the process shows no error messages, but output files are not being generated. I'm running this on a small molecule, about 20 atoms, with the hop

Re: [gmx-users] grompp error: Unknown bond_atomtype

On 4/1/19 5:28 AM, vico...@fizyka.umk.pl wrote: Dear Professor Lemkul, You have written that I mix amber and charmm  forcefields. It is kinda intiguing, becuase I downloaded lipid parameteres in amber and the atom names in the files are exactly the same as charmm-gui pdb output. Atom *na

Re: [gmx-users] grompp error: Unknown bond_atomtype

On 3/26/19 8:22 AM, vico...@fizyka.umk.pl wrote: Hello everyone, I would call myself newbie gromacs user and need some help with task that was given to me. I'm supposed to take protein-ligand complex (bounded by covalence bond) and put it  into membrane. I'm glad I've created the complex in

Re: [gmx-users] grompp error: Unknown bond_atomtype

Cytowanie RAHUL SURESH : On Tue 26 Mar, 2019, 6:18 PM , wrote: Cytowanie RAHUL SURESH : > On Tue 26 Mar, 2019, 6:00 PM , wrote: > >> Hello everyone, >> >> I would call myself newbie gromacs user and need some help with task >> that was given to me. I'm supposed to take protein-ligand comple

Re: [gmx-users] grompp error: Unknown bond_atomtype

On Tue 26 Mar, 2019, 6:18 PM , wrote: > Cytowanie RAHUL SURESH : > > > On Tue 26 Mar, 2019, 6:00 PM , wrote: > > > >> Hello everyone, > >> > >> I would call myself newbie gromacs user and need some help with task > >> that was given to me. I'm supposed to take protein-ligand complex > >> (bounde

Re: [gmx-users] grompp error: Unknown bond_atomtype

Cytowanie RAHUL SURESH : On Tue 26 Mar, 2019, 6:00 PM , wrote: Hello everyone, I would call myself newbie gromacs user and need some help with task that was given to me. I'm supposed to take protein-ligand complex (bounded by covalence bond) and put it into membrane. I'm glad I've created t

Re: [gmx-users] grompp error: Unknown bond_atomtype

On Tue 26 Mar, 2019, 6:00 PM , wrote: > Hello everyone, > > I would call myself newbie gromacs user and need some help with task > that was given to me. I'm supposed to take protein-ligand complex > (bounded by covalence bond) and put it into membrane. I'm glad I've > created the complex in ambe

[gmx-users] grompp error: Unknown bond_atomtype

Hello everyone, I would call myself newbie gromacs user and need some help with task that was given to me. I'm supposed to take protein-ligand complex (bounded by covalence bond) and put it into membrane. I'm glad I've created the complex in amber force field. But now I stucked around me

[gmx-users] Grompp error

Hello everyone I am using gromacs version 2019, and I want to add dihedral restraint to the backbone of the last helix in my protein in my simulation, however grompp gives me this error ERROR 1 [file D2-TorisionRes.itp, line 5]:   Incorrect number of parameters - found 5, expected 3 or 6 for Dih.

Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system

Hi, Mark, I'd be happy to, as soon as I get a chance. I know very little about how GROMACS works internally, but I had a few ideas I wanted to share in the hopes that they might help. One is that pairwise parameters for electrostatics could be implemented in the same way that LJ parameters are st

Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system

Hi, I don't have a solution for the question at hand, but it'd be great to have your inputs attached to a new issue at https://redmine.gromacs.org, so that we can have such an input case to test with, so that we can improve the simplistic implementation! Please upload it if you can. Mark On Fri.

Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system

Scratch that comment about sparseness. I am short on sleep, and for a moment thought I was talking about constraints, not electrostatics. On Fri, Mar 8, 2019 at 1:12 PM Sean Marks wrote: > I understand now, thank you for the prompt response. While the matrix > would actually be quite sparse (sin

Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system

I understand now, thank you for the prompt response. While the matrix would actually be quite sparse (since the constraints are localized to each ice molecule), I take it that memory is being allocated for a dense matrix. That aside, is it feasible to accomplish my stated goal of scaling ice-water

Re: [gmx-users] grompp is using a very large amount of memory on a modestly-sized system

On 3/8/19 11:04 AM, Sean Marks wrote: Hi, everyone, I am running into an issue where grompp is using a tremendous amount of memory and crashing, even though my system is not especially large (63976 atoms). I am using GROMACS 2016.3. My system consists of liquid water (7,930 molecules) next

[gmx-users] grompp is using a very large amount of memory on a modestly-sized system

Hi, everyone, I am running into an issue where grompp is using a tremendous amount of memory and crashing, even though my system is not especially large (63976 atoms). I am using GROMACS 2016.3. My system consists of liquid water (7,930 molecules) next to a block of ice (8,094 molecules). The ic

[gmx-users] grompp Overriding bond parameters and Proper Dih. parameters

Dear users,I used the CGenff and cgenff_charmm2gmx.py to prepare the parameters of a ligand. However, when I run the grompp, the following warnings pop up. As the warning indicates by setting the function type to 9, multiplicity is permitted, if the identical dihedral terms are consecutive (whic

Re: [gmx-users] Grompp errors while changing combination rules

On 7/17/18 5:40 AM, Apramita Chand wrote: Dear All, I had enquired earlier about the steps for changing combination rules in GROMOS ff. As I understood from your answers, if I am to take combination rule 3, I can put sigma and epsilon for my atomtypes under the C6 and C12 columns in ffnonbond

[gmx-users] Grompp errors while changing combination rules

Dear All, I had enquired earlier about the steps for changing combination rules in GROMOS ff. As I understood from your answers, if I am to take combination rule 3, I can put sigma and epsilon for my atomtypes under the C6 and C12 columns in ffnonbonded.itp and these numbers will be interpreted a

Re: [gmx-users] Grompp warning about topology constrains

Thanks Justin Kind Regards,Ahmed Mashaly From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Tuesday, January 30, 2018 6:00 PM Subject: Re: [gmx-users] Grompp warning about topology constrains On 1/30/18 5:46 AM, Ahmed Mashaly wrote: > > Thanks Justin ... The topology

Re: [gmx-users] Grompp warning about topology constrains

[gmx-users] Grompp warning about topology constrains On 1/29/18 11:03 AM, Ahmed Mashaly wrote: Hi, I have set up my parameters with tleap, converted to gromacs with Acpype, did the minimization. For NVT, when I use grompp, this warning appears: WARNING 1 [file gromacs.top, line 79147]:

Re: [gmx-users] Grompp warning about topology constrains

...@gromacs.org Sent: Tuesday, January 30, 2018 2:14 AM Subject: Re: [gmx-users] Grompp warning about topology constrains On 1/29/18 11:03 AM, Ahmed Mashaly wrote: > Hi, > I have set up my parameters with tleap, converted to gromacs with Acpype, did > the minimization. > > > F

Re: [gmx-users] Grompp warning about topology constrains

On 1/29/18 11:03 AM, Ahmed Mashaly wrote: Hi, I have set up my parameters with tleap, converted to gromacs with Acpype, did the minimization. For NVT, when I use grompp, this warning appears: WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of an angle, connected by c

[gmx-users] Grompp warning about topology constrains

Hi, I have set up my parameters with tleap, converted to gromacs with Acpype, did the minimization. For NVT, when I use grompp, this warning appears: WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of an angle, connected by constraints and  with masses that differ by mor

Re: [gmx-users] Grompp error : Incorrect number of parameters

Hi, The large energy means your topology is probably broken. Please use a tool that will write an .itp file for you (e.g. SwissParam?), or next time get your topology for your ligand working before you try to use it in a complex. Even get a simple form of the ligand working first, to teach yoursel

Re: [gmx-users] Grompp error : Incorrect number of parameters

To be included here, the ligand I have uploaded seems to be so congested and out of form. Look literally like a clumsy ball. I am not sure what make this happen. On Wed, Dec 20, 2017 at 2:51 PM, RAHUL SURESH wrote: > Dear Alex > > I have tried that but the system collapse. For em_real.mdp option

Re: [gmx-users] Grompp error : Incorrect number of parameters

Dear Alex I have tried that but the system collapse. For em_real.mdp option,I get message stating Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a

Re: [gmx-users] Grompp error : Incorrect number of parameters

The description for the Urey-Bradley potential (assuming two quadratic terms qualify for the proud term "potential") is described in the user manual, and the constants' order of appearance in the itp file is given in the Table 5.5 of the manual. If you have a basic quadratic angular term (first

Re: [gmx-users] Grompp error : Incorrect number of parameters

Hi Thank you Mark. On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham wrote: > Hi, > > Sorry I don't know how any of these non-GROMACS tools work, or even whether > they actually generate Urey Bradley interactions that have all the terms. I > suggest you spend some time with the documentation. > >

Re: [gmx-users] Grompp error : Incorrect number of parameters

Hi, Sorry I don't know how any of these non-GROMACS tools work, or even whether they actually generate Urey Bradley interactions that have all the terms. I suggest you spend some time with the documentation. Mark On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH wrote: > Sorry Mark, I failed to note

Re: [gmx-users] Grompp error : Incorrect number of parameters

Sorry Mark, I failed to note that. I am afraid that I don't know what that are those components and how and where to find it. If you are actually meaning about "ub0 kub" components, how could i find the value for it. In case of swiss param generated itp file, these components appear to be 0. Any

Re: [gmx-users] Grompp error : Incorrect number of parameters

Hi, Please read my answer. Mark On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH wrote: > On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul wrote: > > > > > > > On 12/19/17 11:14 AM, RAHUL SURESH wrote: > > > Dear all > > > > > > For grompp em.mdp I get an error > > > > > > ERROR 1 [file THC.itp, line

Re: [gmx-users] Grompp error : Incorrect number of parameters

On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul wrote: > > > On 12/19/17 11:14 AM, RAHUL SURESH wrote: > > Dear all > > > > For grompp em.mdp I get an error > > > > ERROR 1 [file THC.itp, line 89]: > >Incorrect number of parameters - found 2, expected 4 or 8 for U-B. > > > > My itp file as foll

Re: [gmx-users] Grompp error : Incorrect number of parameters

Hi, The CHARMM software implements UB with two separate bond and angle components, which you probably have to find and to insert here, to suit the way GROMACS implements the interaction in a self-contained way. Mark On Wed, Dec 20, 2017, 10:36 AM Justin Lemkul wrote: > > > On 12/19/17 11:14 AM

Re: [gmx-users] Grompp error : Incorrect number of parameters

On 12/19/17 11:14 AM, RAHUL SURESH wrote: Dear all For grompp em.mdp I get an error ERROR 1 [file THC.itp, line 89]: Incorrect number of parameters - found 2, expected 4 or 8 for U-B. My itp file as follows [ angles ] 1 2 29 579.178 109.588 *{Line 89}* 1 2 3 5

[gmx-users] Grompp error : Incorrect number of parameters

Dear all For grompp em.mdp I get an error ERROR 1 [file THC.itp, line 89]: Incorrect number of parameters - found 2, expected 4 or 8 for U-B. My itp file as follows [ angles ] 1 2 29 579.178 109.588 *{Line 89}* 1 2 3 532.192 112.817 2 3 31 551.424 10

[gmx-users] Grompp error : Incorrect number of parameters

Dear all For grompp em.mdp I get an error ERROR 1 [file THC.itp, line 89]: Incorrect number of parameters - found 2, expected 4 or 8 for U-B. My itp file as follows [ angles ] 1 2 29 579.178 109.588 *{Line 89}* 1 2 3 532.192 112.817 2 3 31 551.424 10

[gmx-users] grompp/COM Pulling- Is number of pull groups an issue, an issue with the free energy of the molecule, or is there a limit to the size of the whole structure?

Hello! I'm trying to grompp my files that has around 140 pull groups, but whenever I try to pull more than 128 groups together, the grompp command stops between *Largest charge group radii for Van der Waals: 0.149, 0.149 nm* *Largest charge group radii for Coulomb: 0.165, 0.164 nm* and what

Re: [gmx-users] grompp error

My guess would be that when you thought ran it with the increased box size coordinate file, you actually used the original coordinate file. FYI http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_eleme

[gmx-users] grompp error

Dear Gromacs users, I got the following error when I tried to run grompp. ERROR 1 [file system.top, line 18]: ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist I increased the box size and re-tried to run grompp,but it didn't work.

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

Done Mark, thanks. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every proble

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

Hi, I'm sure we have opportunities to improve this code - please do file a redmine issue with repro inputs so we can profile and see! Thanks, Mark On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul wrote: > > > On 10/2/17 11:14 PM, Dallas Warren wrote: > > Thanks for the reply Justin. > > > > I am

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

On 10/2/17 11:14 PM, Dallas Warren wrote: Thanks for the reply Justin. I am just going to use the largest exclusion bond distance I can, then ignore the RDF of those beyond that distance. Seems curious to me (not actually understanding what grommp is generating) that the list is so large. Th

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

Thanks for the reply Justin. I am just going to use the largest exclusion bond distance I can, then ignore the RDF of those beyond that distance. Seems curious to me (not actually understanding what grommp is generating) that the list is so large. These are linear molecules, 38 atoms, 60 molecul

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

On 9/28/17 12:25 AM, Dallas Warren wrote: Justin, No, I have separate index groups for each of the atom types. Wouldn't that still have the pair of atoms that are located on the same molecule, contributing to the RDF? Molecule is like this: C1 ---C38 Index file would be something like t

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

Justin, No, I have separate index groups for each of the atom types. Wouldn't that still have the pair of atoms that are located on the same molecule, contributing to the RDF? Molecule is like this: C1 ---C38 Index file would be something like this: [ C1 ] 1 39 77 . [ C38 ] 38 76 114 .

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

On 9/27/17 7:54 PM, Dallas Warren wrote: Left the 37 one running, and it ended up being "Killed". Was distracted, so didn't really see how long it ran etc, but suspect it was due to amount of memory being used up. I am going about this the right way? i.e. want the RDF between atoms at either e

Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

Left the 37 one running, and it ended up being "Killed". Was distracted, so didn't really see how long it ran etc, but suspect it was due to amount of memory being used up. I am going about this the right way? i.e. want the RDF between atoms at either end of the molecule (38 atoms long), and don't

[gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

Just want to check that this should be taking as long as it is (expected behaviour etc), for grompp to generate the tpr when nrexcl is large. I have a long straight chain molecule with 38 atoms that are generating RDFs for, so need to change the [ moleculetype ] nrexcl to exclude atoms within the

[gmx-users] grompp warning

Hello GMX users, I added another ligand as a new residue in the topology database, and then build the topology of the liand with pdb2gmx, everything worked well. But I got this warning from grompp for a nvt equilibration after successful minimizations: There are atoms at both ends of an ang

Re: [gmx-users] Grompp error for graphene modeling

Thanks Justin for your help. I will modify the force field again to model the particles better. Best,Mohammad From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Saturday, 27 May 2017, 23:20:26 Subject: Re: [gmx-users] Grompp error for graphene modeling On 5/27/17 3:33 AM

Re: [gmx-users] Grompp error for graphene modeling

On 5/27/17 3:33 AM, ‪Mohammad Roostaie‬ ‪ wrote: Hi All, I modeled graphene in a box of water with a peptide in the center of the box. I modified the OPLS-AA force field by adding the parameters from this link to the modified force field: http://chembytes.wikidot.com/grocnt. But, when I want

[gmx-users] Grompp error for graphene modeling

Hi All, I modeled graphene in a box of water with a peptide in the center of the box. I modified the OPLS-AA force field by adding the parameters from this link to the modified force field: http://chembytes.wikidot.com/grocnt. But, when I want to add ions to the system, I got this warning: WARNI

[gmx-users] grompp error

Hi GROMACS users,   I want to simulate a graphene sheet, and I want to use OPLS-AA force field. So, I copied the forcefield in my directory and changed some the files in it (ffbonded.itp, ffnonbonded.itp, atomtype.atp, aminoacids.rtp, and atomname2type.n2t). I used the pdb2gmx command to creat

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Issue #2077 created, thanks! On Tue, Nov 15, 2016 at 11:11 AM, Mark Abraham wrote: > Hi, > > Yes that seems a bit inconsistent. Please file a redmine and include e.g. a > tarball of suitable inputs to reproduce what's going on within grompp. > > Mark > > On Tue, Nov 15, 2016 at 3:01 PM Elton Carv

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Hi, Yes that seems a bit inconsistent. Please file a redmine and include e.g. a tarball of suitable inputs to reproduce what's going on within grompp. Mark On Tue, Nov 15, 2016 at 3:01 PM Elton Carvalho wrote: > Hi, Mark, > > Actually, there seems to be a bug somewhere, because if I defined >

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Hi, Mark, Actually, there seems to be a bug somewhere, because if I defined three type 9 dihedrals in a file and then I define the same three type 9 dihedrals later on, there should be three warnings: one for each multiplicity. there were only two warnings, which means the first one somehow is sil

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Hi, Ok that makes sense. Otherwise it would have seemed like it had to be a code bug. Maybe we could add a warning for including the same file twice? Does anybody do that deliberately E.g with different preprocessor variables defined? Mark On Tue, 15 Nov 2016 00:30 Elton Carvalho wrote: > My

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

My apologies, After careful inspection, I noticed that I had #included a copy of this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [ dihedraltypes ] directive is actually loaded twice, hence the warnings. Removing the #include from forcefield.itp and keeping it in the .top file elim

[gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

Hello, fellow Gromacs Users, I'm trying to model P3DDT with CGenFF according to the instructions at paramchem.org, running the cgenff_charmm2gmx.py script as provided in their website. All this is being done on gromacs 2016. The script converts the .str file generated by paramchem.org to gromacs

Re: [gmx-users] grompp error (segmentation fault)in gromacs version 5.0.6

On 8/9/16 2:51 AM, iamdsoumi wrote: Hi, I carry on md run on protein-dna complex using AMBER99SB-ILDN force field. Here I state my problem. gmx_mpi pdb2gmx -f em267.pdb -o em267_processed.gro -p topol.top -water tip3p -ignh it compile successfully. gmx_mpi editcon

[gmx-users] grompp error (segmentation fault)in gromacs version 5.0.6

Hi, I carry on md run on protein-dna complex using AMBER99SB-ILDN force field. Here I state my problem. gmx_mpi pdb2gmx -f em267.pdb -o em267_processed.gro -p topol.top -water tip3p -ignh it compile successfully. gmx_mpi editconf -f em267_processed.gro -o em267_newbox

[gmx-users] grompp error(Segmentation fault)in gromacs version 5.0.6

Hi,    I carry on md run on protein-dna complex using  AMBER99SB-ILDN force field. Here I state my problem.   gmx_mpi pdb2gmx -f em267.pdb -o em267_processed.gro -p topol.top -water tip3p -ignh  it compile successfully.  gmx_mpi editconf -f em267_processed.gro -o em267_newbox.

Re: [gmx-users] grompp 5.1.3 chokes on multiple tau_p for semiisotropic pcoupltype

Hi, Yes that's now the correct behaviour, as a side effect of fixing a bug where you could pass 0.8 to an integral parameter and it would silently interpret it as 0... Mark On Tue, 26 Jul 2016 20:50 David Dotson wrote: > Ah, I see now. tau-p only gets a single value, but compressibility and >

Re: [gmx-users] grompp 5.1.3 chokes on multiple tau_p for semiisotropic pcoupltype

Ah, I see now. tau-p only gets a single value, but compressibility and ref-p get a value for each of the two directions. Doing this yields no errors. Thanks Justin! David On 07/26/2016 11:45 AM, Justin Lemkul wrote: > > > On 7/26/16 2:39 PM, David Dotson wrote: >> Greetings, >> >> Using gromac

Re: [gmx-users] grompp 5.1.3 chokes on multiple tau_p for semiisotropic pcoupltype

On 7/26/16 2:39 PM, David Dotson wrote: Greetings, Using gromacs 5.1.3's `gmx grompp` on the MDP file below (also attached) with `gmx grompp -c start.gro -f premd.mdp -p system.top -n index.ndx`: ; Gromacs mdp file include = -I. -I.. -I../top define

[gmx-users] grompp 5.1.3 chokes on multiple tau_p for semiisotropic pcoupltype

Greetings, Using gromacs 5.1.3's `gmx grompp` on the MDP file below (also attached) with `gmx grompp -c start.gro -f premd.mdp -p system.top -n index.ndx`: ; Gromacs mdp file include = -I. -I.. -I../top define = integrator = sd

Re: [gmx-users] grompp not enough parameters

Thanks a lot ... I feel really dumb here ~~ Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-06-15 17:26 GMT+02:00 Justin Lemkul : > > > On 6/15/16 11:07 AM, Marlon Sidore wrot

[gmx-users] grompp not enough parameters

Hi Marlon, If you change the comma into a point in the force constant values it should work Good luck Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file clus

Re: [gmx-users] grompp not enough parameters

On 6/15/16 11:07 AM, Marlon Sidore wrote: Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file clusters_ffbonded.itp, line 53]: Not enough parameters ERROR 2 [file clusters_ffbonde

[gmx-users] grompp not enough parameters

Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file clusters_ffbonded.itp, line 53]: Not enough parameters ERROR 2 [file clusters_ffbonded.itp, line 54]: Not enough parameters ERR

Re: [gmx-users] Grompp error

Thanks a lot for your insight. I will redefine them. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Mon, May 30, 2016 at 8:26 PM, Justin Lemkul wrote: > > > On 5/30/16 10:55 AM, Anurag Dobhal wrote: > >> Th

Re: [gmx-users] Grompp error

On 5/30/16 10:55 AM, Anurag Dobhal wrote: Thanks a lot for your reply. I have set tc-groups as tc-grps = Other acetone ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each Then you can't

Re: [gmx-users] Grompp error

Thanks a lot for your reply. I have set tc-groups as tc-grps = Other acetone ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *

Re: [gmx-users] Grompp error

On 5/30/16 10:40 AM, Anurag Dobhal wrote: Dear Gromacs users I am solvating my molecule ( a ploymer chain, having 78 atoms) in Propan-2-one [ molecules] = acetone. I have already updated [ molecules ] section in the topology file (topol.top) after the solvation step. after the sucessful ener

[gmx-users] Grompp error

Dear Gromacs users I am solvating my molecule ( a ploymer chain, having 78 atoms) in Propan-2-one [ molecules] = acetone. I have already updated [ molecules ] section in the topology file (topol.top) after the solvation step. after the sucessful energy minimization step, while runing grompp I am

Re: [gmx-users] grompp protein-ligand complex simulation

Justin Lemkul [jalem...@vt.edu] Sent: Thursday, March 3, 2016 11:04 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] grompp protein-ligand complex simulation On 3/3/16 12:00 AM, Adamu, Aliyu wrote: > Thanks Justin for the response. no my protein does not have any Zn2+ bound. > as f

Re: [gmx-users] grompp protein-ligand complex simulation

s.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Tuesday, March 1, 2016 7:21 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] grompp protein-ligand complex simulation On 3/1/16 5:06 AM, Adamu, Aliyu wrote: Hi all, I am trying to run protein-

Re: [gmx-users] grompp protein-ligand complex simulation

ys.kth.se] on behalf of Justin > Lemkul [jalem...@vt.edu] > Sent: Tuesday, March 1, 2016 7:21 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] grompp protein-ligand complex simulation > > On 3/1/16 5:06 AM, Adamu, Aliyu wrote: > > Hi all, > > > > I am tryin

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