Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Justin, The command line that got fatal error is: gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh -merge interactive The command line that works fine is: gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge interactive (just

Re: [gmx-users] Error with moleculetype

On 5/19/17 6:03 PM, Pandya, Akash wrote: Tried to put it at the end but it still came up with the same error. Justin, I don't understand what you mean? If the file has been edited with a non-plain text editor then you can have malformed return characters. Make sure you only ever edit

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

On 5/19/17 6:31 PM, ZHANG Cheng wrote: Dear Justin, I replied the thread already, but it is waiting for approval due to large email content. Could you please approve it? I have no control over that. If it's too much for an email (normally pdb2gmx output is fine) then upload to e.g.

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Justin, I replied the thread already, but it is waiting for approval due to large email content. Could you please approve it? Cheng ---Original--- From: "ZHANG Cheng"<272699...@qq.com> Date: 2017/5/19 22:37:52 To: "gromacs.org_gmx-users"; Cc:

Re: [gmx-users] Error with moleculetype

Tried to put it at the end but it still came up with the same error. Justin, I don't understand what you mean? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent:

Re: [gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

On 5/19/17 5:37 PM, ZHANG Cheng wrote: Dear Gromacs, I got this fatal error after running "pdb2gmx": Please provide your exact command and full screen output. There's a lot of relevant information there, because pdb2gmx is doing a lot of complex things. -Justin Fatal error: Residue 1

Re: [gmx-users] Need to confirm parameters.

On 5/19/17 8:22 AM, Sailesh Bataju wrote: Hi Sir, You mean like choosing OPLS forcefield for all-atom model would be moer appropriate for me? At minimum, some all-atom force field, because whatever you were doing before has no relationship to GROMOS and is unlikely to succeed. Isobutane

[gmx-users] pdb2gmx: Atom N used in the topology not found in the input (PDB) file

Dear Gromacs, I got this fatal error after running "pdb2gmx": Fatal error: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote: First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file I found different linkages for beta-glucose, but non for alpha-glucose. I am trying to make a simple chain with 1->4 linkages like below:

Re: [gmx-users] Error with moleculetype

On 5/19/17 5:33 PM, Mark Abraham wrote: Hi, Ok. Maybe it needs to be last in the molecules? Or perhaps the error points to a malformed line ending that causes genion to choke when updating the topology. -Justin Mark On Fri, 19 May 2017 23:19 Pandya, Akash

Re: [gmx-users] Error with moleculetype

Hi, Ok. Maybe it needs to be last in the molecules? Mark On Fri, 19 May 2017 23:19 Pandya, Akash wrote: > It was the genion command. Here is the message. > > Fatal error: > No line with moleculetype 'SOL' found the [ molecules ] section of file > 'topol.top' > >

Re: [gmx-users] Error with moleculetype

It was the genion command. Here is the message. Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On

Re: [gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

Hi, Historically that was how things were done. Nobody thinks it is a good idea any more. Use the Verlet scheme plus the recommendations for CHARMM forcefields in GROMACS and you'll be fine - charge groups are removed perforce. Mark On Fri, 19 May 2017 18:44 Dawid das

[gmx-users] Error with moleculetype

Hi all, I have received an error message shown below. Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I don't

[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

Dear Gromacs Users, I am a bit confused whether I shouldn't use charge group-based cut-off for electrostatics when using CHARMM22. If I shouldn't use it, what is the purpose of specification of charge groups in original CHARMM files? Best wishes, Dawid -- Gromacs Users mailing list * Please

[gmx-users] Nonequilibrium simulations

Hello, I am running non-equilibrium simulations using the "acc-groups" command and the Nose-Hoover thermostat. I just wanted to confirm that in Gromacs code this additional acceleration is not considered to contribute to the temperature when velocities are adjusted. Thank you! Jon -- Gromacs

Re: [gmx-users] Graphene modeling

Hi Justin, Thank you very much. It is Ok now. Best,Mohammad From: Justin Lemkul To: Discussion list for GROMACS users Sent: Tuesday, 16 May 2017, 18:34:14 Subject: Re: [gmx-users] Graphene modeling On 5/16/17 7:31 AM, ‪Mohammad Roostaie‬ ‪

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file I found different linkages for beta-glucose, but non for alpha-glucose. I am trying to make a simple chain with 1->4 linkages like below: alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.

Re: [gmx-users] Need to confirm parameters.

Hi Sir, You mean like choosing OPLS forcefield for all-atom model would be moer appropriate for me? Thank you. On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju wrote: > Hi Sir/Ma'am, > > I've finally created parameter file of isobutane using gromos54a7 > forcefield for

[gmx-users] Regarding sampling convergence

Dear users, I have a 100 ns simulation trajectory and I have generated FEL (free energy landscape) with it to extract a minimum energy conformation of my protein. How can I show sampling convergence of FEL in gromacs? Do I have to split the trajectory (say at every 20ns) and generate FELs from

Re: [gmx-users] ligand moving out during umbrella sampling

On 5/19/17 5:56 AM, abhisek Mondal wrote: On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul wrote: On 5/17/17 8:55 AM, abhisek Mondal wrote: This time I think I got ligand restrained successfully during the umbrella sampling. I have removed the restrain from protein, as

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

On 5/18/17 6:35 PM, Mohammad Hassan Khatami wrote: Thanks Justin. I have tried the CHARMM-GUI but it crashed. I might need to modify the order of the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have downloaded the “toppar_c36_feb16” but I did not find a manual on how

Re: [gmx-users] Need to confirm parameters.

On 5/19/17 7:30 AM, Sailesh Bataju wrote: Hi Sir/Ma'am, I've finally created parameter file of isobutane using gromos54a7 forcefield for all-atom model. Some of the parameters for bond angle parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp file in the relevant

[gmx-users] Need to confirm parameters.

Hi Sir/Ma'am, I've finally created parameter file of isobutane using gromos54a7 forcefield for all-atom model. Some of the parameters for bond angle parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp file in the relevant forcefield, instead I used FTFE - CTFE - FTFE and

Re: [gmx-users] ligand moving out during umbrella sampling

On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul wrote: > > > On 5/17/17 8:55 AM, abhisek Mondal wrote: > >> This time I think I got ligand restrained successfully during the umbrella >> sampling. I have removed the restrain from protein, as per your advice. >> Defined the COM