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

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

[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

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

[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:

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

[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

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

[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 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

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

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

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 > >>

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

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

[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

[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

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

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

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

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

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

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: >

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

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. > > > >

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

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

[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

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

[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

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 <jalem...@vt.edu> To: gmx-us...@gromacs.org Sent: Saturday, 27 May 2017, 23:20:26 Subject: Re: [gmx-users] Grompp error for graphene modeling O

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:

[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

[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

[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.gro -c -d 1.0 -bt

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

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

[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

Re: [gmx-users] grompp error

All Deadr Hi we want to run a protein-ligand MD simulation, when we use mdrun (mdrun -s em.tpr -nt 4 -o em.trr -c complexpr.gro -e em.edr) we have not any error but the run written killed: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 400 Killed can anyone help please?

Re: [gmx-users] grompp error

Hi, That's happening somewhere outside GROMACS. Talk to your sysadmins. Mark ‪On Tue, Nov 10, 2015 at 9:17 AM ‫محمد گره گشا‬‎ wrote:‬ > All Deadr > > Hi > > we want to run a protein-ligand MD simulation, when we use mdrun (mdrun -s > em.tpr -nt 4 -o em.trr -c

Re: [gmx-users] grompp error

On 10/18/15 3:15 AM, محمد گره گشا wrote: All dears we run MD for protein-ligand complex that we take from Autodock. but when we run grompp we face this error: ERROR 1 [ file LIG.itp, line 401 ] No default Proper Dih. types Fatal error: There was 1 error in input file(s) can any 1 help we

[gmx-users] grompp error

All dears we doing MD by oplsa ff for protein-ligand complex that we take from Autodock. we do this steps to add ligand as a residue at residue database, but when run grompp we face this error ERROR 1 [ file LIG.itp, line 401 ]: No default proper Dih. types Fatal error: There was 1

[gmx-users] grompp error

All dears we doing MD by oplsa ff for protein-ligand complex that we take from Autodock. we do this steps to add ligand as a residue at residue database, but when run grompp we face this error ERROR 1 [ file LIG.itp, line 401 ]: No default proper Dih. types Fatal error: There was 1

[gmx-users] grompp error

All dears we run MD for protein-ligand complex that we take from Autodock. but when we run grompp we face this error: ERROR 1 [ file LIG.itp, line 401 ] No default Proper Dih. types Fatal error: There was 1 error in input file(s) can any 1 help we to resolve this error pleas? we attached

Re: [gmx-users] grompp error

On 9/14/15 4:30 AM, faride badalkhani wrote: Dear GROMACS users, I need to simulate a hyper branched polymer (a polyamidoamine dendrimer). I used the GROMOS53A6 to perform the simulation. But, I have a problem with defining the angles and dihedrals that are between two residues (because of

[gmx-users] grompp error

Dear GROMACS users, I need to simulate a hyper branched polymer (a polyamidoamine dendrimer). I used the GROMOS53A6 to perform the simulation. But, I have a problem with defining the angles and dihedrals that are between two residues (because of dendrimers hyper branched structure). I can perform

[gmx-users] Grompp Error No default Ryckaert-Bell. types

Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error No default Ryckaert-Bell. types. I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default Ryckaert-Bell. types. but on checking

Re: [gmx-users] Grompp Error No default Ryckaert-Bell. types

On 7/10/15 9:47 AM, Anurag Dobhal wrote: Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error No default Ryckaert-Bell. types. I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default

[gmx-users] Grompp error No default Ryckaert-Bell. types

Hello all How can I address the No default Ryckaert-Bell. types error. The error is also in between the atoms which are not bonded with each other. Thank you -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever. Alex Thank you for your reply. I am simulating a PLGA (poly lactic co-glycolic acid molecle). I get the topology file and I solvated the molecule. my system is neutral.

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

"Which angles?" -- wait until Mark Abraham gets here. You must have a very special version of aminoacids.rtp Example: https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp Thank you But which angles I need to add in .rtp file. are you talking about

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

On 5/4/15 4:20 AM, Alex wrote: The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL required to define connectivity. Remaining bonded interactions are then deduced JL from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL those values are used, instead. If an

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

On 5/4/15 1:06 PM, Alex wrote: JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL required to define connectivity. Remaining bonded interactions are then deduced JL from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL those

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

True, thats why i mentioned Mark.:-) In all honesty, though, for small molecules, i would prefer to ignore the new format and actually add everything in the rtp entry to make ffbonded look like less of a zoo. Also, it was late night of extreme gromacs intercourse for me, which finally paid off.

[gmx-users] grompp error - no molecules were defined in the system

When running grompp, I am receiving the error No molecules were defined in the system. I have a relatively simple topology and .gro file. I cannot locate the source of the error. Does anyone have any suggestions? Here is an example of the .gro and .top file that I am using. Thanks. HSb 1

Re: [gmx-users] grompp error - no molecules were defined in the system

On 1/18/14, 2:20 PM, rankinb wrote: When running grompp, I am receiving the error No molecules were defined in the system. I have a relatively simple topology and .gro file. I cannot locate the source of the error. Does anyone have any suggestions? Here is an example of the .gro and .top