Re: [gmx-users] pdb2gmx: Selecting Force Field in first command

On 4/10/20 9:03 PM, ferna...@hypernetlabs.io wrote: Hi all! Context I'm trying to run simple gromacs example commands below * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc In a

[gmx-users] pdb2gmx: Selecting Force Field in first command

Hi all! Context I'm trying to run simple gromacs example commands below * gmx pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water spce * gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc In a Docker container with a Dockerfile (Dockerfile = instruction

Re: [gmx-users] pdb2gmx command not found

Versions of GROMACS for awhile now have moved all the scripts underneath "gmx". So now you need use "gmx pdb2gmx" On Fri, 20 Mar. 2020, 5:28 am Sutanu L'Étranger, < schrodingerscat...@gmail.com> wrote: > Hi, > > I've recently installed gromacs latest version, but when I type pdb2gmx, it > shows

[gmx-users] pdb2gmx command not found

Dear Sutanu: try "gmx pdb2gmx" instead. Most older stand-alone commands are now run as options to the gmx command, so pdb2gmx is now gmx pdb2gmx and g_order is now gmx order. Good luck, Chris. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] pdb2gmx command not found

Hi, I've recently installed gromacs latest version, but when I type pdb2gmx, it shows "pdb2gmx command not found", please advise. Thank you. Regards, Sutanu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] pdb2gmx - generating topology for helicase-DNA complex (3PJR)

Dear GMX-Users, Firstly, in light of the current situation with CoVID-19 I would like to wish everyone the best of luck with staying healthy and safe during these uncertain times. Now on to my Gromacs issue: I am relatively new to Gromacs and molecular dynamics. For my research I am

Re: [gmx-users] pdb2gmx - generating topology for helicase-DNA complex (3PJR)

On 3/17/20 1:00 PM, Max Winokan wrote: Dear GMX-Users, Firstly, in light of the current situation with CoVID-19 I would like to wish everyone the best of luck with staying healthy and safe during these uncertain times. Now on to my Gromacs issue: I am relatively new to Gromacs

Re: [gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain

On 2/7/20 8:38 AM, i.i...@bioc.uzh.ch wrote: Dear gmx users, I am trying to simulate a complex consisting of DNA and a protein. One chain is methylated at C. The methylated cytosine is included in the newest Charmm36 forcefield as D5MC, yet somehow when I do "gmx pdb2gmx" Gromacs does

[gmx-users] pdb2gmx charmm36 + methylated cytosine breaks DNA chain

Dear gmx users, I am trying to simulate a complex consisting of DNA and a protein. One chain is methylated at C. The methylated cytosine is included in the newest Charmm36 forcefield as D5MC, yet somehow when I do "gmx pdb2gmx" Gromacs does not recognize the methylated C as part of the

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

On 1/17/20 4:25 AM, András Ferenc WACHA wrote: Dear Justin, there are no name clashes in the .rtp files by design, I never re-use already existing residue names. Beta3-homo-lysine is B3K, beta2-homo-lysine is B2K, and disubstituted amino-acids also have their naming scheme. Sorry, no idea.

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

Dear Justin, there are no name clashes in the .rtp files by design, I never re-use already existing residue names. Beta3-homo-lysine is B3K, beta2-homo-lysine is B2K, and disubstituted amino-acids also have their naming scheme. Andras On 1/16/20 11:34 PM, Justin Lemkul wrote: > > > On 1/16/20

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

On 1/16/20 10:07 AM, András Ferenc WACHA wrote: Dear Justin, thank you. Am I doing something wrong or is this a bug in Gromacs? Do you have a suggestion how to make this work? Should I rename the terminal patches or should I put everything under one basename (sacrificing cleanliness and

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

Dear Justin, thank you. Am I doing something wrong or is this a bug in Gromacs? Do you have a suggestion how to make this work? Should I rename the terminal patches or should I put everything under one basename (sacrificing cleanliness and maintainability)? Kind regards, Andras On 1/16/20 2:47

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

On 1/16/20 8:44 AM, András Ferenc WACHA wrote: Sorry, now replying to the whole list: Dear Justin, I have obtained the base force field from the website of the MacKerell Lab (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz). I have checked

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

Sorry, now replying to the whole list: Dear Justin, I have obtained the base force field from the website of the MacKerell Lab (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz). I have checked and the merged.n.tdb file is the same in my version

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

On 1/16/20 8:04 AM, András Ferenc WACHA wrote: Dear fellow Gromacs users, I have developed an extended version of the CHARMM36m force field for beta-amino acids (https://charmm-betaff.readthedocs.io, https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found pdb2gmx works well.

[gmx-users] pdb2gmx picks up the wrong .tdb files?

Dear fellow Gromacs users, I have developed an extended version of the CHARMM36m force field for beta-amino acids (https://charmm-betaff.readthedocs.io, https://gitlab.com/awacha/charmm-beta.ff). For beta-amino acids I found pdb2gmx works well. However, if I try to use it for natural peptides and

Re: [gmx-users] pdb2gmx , or equivalent

On 11/15/19 5:15 PM, Ling Chan wrote: I see, thank you Justin. Suppose you mean ASP vs ASH, HID, HIE, HIP, etc.? Yes, as well as all the constituent hydrogen atoms. But how about disulfide bridges? Does pdb2gmx respect SSBOND and / or CONECT records in the PDB? Perhaps it will

[gmx-users] pdb2gmx , or equivalent

I see, thank you Justin. Suppose you mean ASP vs ASH, HID, HIE, HIP, etc.? But how about disulfide bridges? Does pdb2gmx respect SSBOND and / or CONECT records in the PDB? Perhaps it will re-evaluate them regardless? Also, I see on the pdb2gmx manual page that the default glutamine is charged.

Re: [gmx-users] pdb2gmx , or equivalent

On 11/15/19 12:48 PM, Ling Chan wrote: Hello Colleagues, I would like to run Gromacs on some proteins that I have prepared. I see that you can obtain Gromacs input files using pdb2gmx. Just wonder if one can prevent pdb2gmx from tempering with your protein? I mean, pdb2gmx does a bunch of

[gmx-users] pdb2gmx , or equivalent

Hello Colleagues, I would like to run Gromacs on some proteins that I have prepared. I see that you can obtain Gromacs input files using pdb2gmx. Just wonder if one can prevent pdb2gmx from tempering with your protein? I mean, pdb2gmx does a bunch of clean ups. I would like it to skip the

Re: [gmx-users] pdb2gmx error due to terminal capping of peptide

Hi, Leave the rtp the way it was and name the residue in the pdb file so that it matches. Then you won't have to teach pdb2gmx that your newly invented residue is protein Mark On Fri., 25 Jan. 2019, 05:51 Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hi GMX users, > > >

[gmx-users] pdb2gmx error due to terminal capping of peptide

Hi GMX users, 1. I drew the structure of my target peptide on Pymol, added amide capping group (NHH) at C terminus of peptide 2. Typed in the command: gmx pdb2gmx –f A15K.pdb –o A15K.gro –ter –ignh 3. Chose AMBER99sb-ildn force field which has parameters for NH2 capping group 4.

Re: [gmx-users] pdb2gmx fatal error

Dear Justin, Thank you for your full explanation. That made it all clear now. Kind regards, Ali > On 13 Nov 2018, at 00:57, Justin Lemkul wrote: > > > > On 11/8/18 1:37 PM, Ali Khodayari wrote: >> Dear Justin, >> >> Thank you for your response. Yet, I have not been able to solve the

Re: [gmx-users] pdb2gmx fatal error

On 11/8/18 1:37 PM, Ali Khodayari wrote: Dear Justin, Thank you for your response. Yet, I have not been able to solve the problem. The structure looks fine but gromacs is complaining about a dangling atom at one of the terminal ends, if I choose no terminal to be added. While, You can't

Re: [gmx-users] pdb2gmx fatal error

...@gromacs.org Subject: Re: [gmx-users] pdb2gmx fatal error On 11/7/18 1:05 PM, Ali Khodayari wrote: > Dear gmx users, > > > > I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom > names were modified according to the rtp file of the force field. Yet, > I get the fo

[gmx-users] pdb2gmx fatal error

Dear gmx users, I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom names were modified according to the rtp file of the force field. Yet, I get the following error while I perform pdb2gmx command: Fatal error: Residue 4 named GLC of a molecule in the input file was

Re: [gmx-users] pdb2gmx charmm issue with version 2018.3

On 10/12/18 8:10 PM, Akshay wrote: Hello All, I have been using Gromacs version 2016 and upgraded this week to 2018.3. In the new version, I am having an issue with pdb2gmx. My file is a series of protein chains and finally a dna-double helix like the following chain A - Protein chain B -

Re: [gmx-users] pdb2gmx: how to preserve original ions?

minal option %s:%s for residue %s"%(v,k,resname)) if not found: print("Unknown option but trying anyway:",selectedOption) p.sendline(selectedOption) except pexpect.EOF: print(p.before) except pexpect.TIMEOUT: print("TIMEOUT"

Re: [gmx-users] pdb2gmx: how to preserve original ions?

Hi, The name of the residue in that force fields aminoacids.rtp is CLA, which is the only thing pdb2gmx can understand. Otherwise your procedure should just work if you rename your ion residues appropriately. Do let us know how you go! Mark On Wed, Jul 18, 2018, 03:23 Anderson, Amos wrote: >

Re: [gmx-users] pdb2gmx: how to preserve original ions?

On 7/17/18 9:22 PM, Anderson, Amos wrote: Hi Gromacs users, I’ve never used gromacs before, so sorry if this question has an obvious answer somewhere — it seems like the sort I should have been able to find an answer for… I want to write a python script to prepare an arbitrary pdb for use

[gmx-users] pdb2gmx: how to preserve original ions?

Hi Gromacs users, I’ve never used gromacs before, so sorry if this question has an obvious answer somewhere — it seems like the sort I should have been able to find an answer for… I want to write a python script to prepare an arbitrary pdb for use with gromacs (e.g., does these steps

[gmx-users] pdb2gmx with CHARMM-GUI output

Hi, I'd like to use pdb2gmx, mainly to add virtual sites to an existing system, either pre-equilibrated (in CHARMM) or a new system from CHARMM-GUI. Is pdb2gmx suitable for this? The issue Im coming across is that, choosing the CHARMM27 forcefield, the POPC lipids have a different naming

Re: [gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

Hi again, It seems from previous posts that this type of system setup is of general interest so I thought I'd share the solution(s). I modified the tdb file for the 5' end, here for CHARMM27, by adding the following to the end of dna.n.tdb [ hack ] [ replace ] C5' C5' CN8B12.011

[gmx-users] pdb2gmx "dangling bond" error when trying to make periodically connected DNA

Hi, I'm trying to create a topology for DNA with periodically connected ends. There's a previous message on this, with advice by Justin: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096970.html I have a single-stranded DNA structure in a pdb file with a phosphate on

Re: [gmx-users] Pdb2gmx melts molecules due to bad distances

Thanks, but it doesn't work. Same problem. Gianmarco Bartalini Il 27 nov 2017 14:37, "Justin Lemkul" ha scritto: > > > On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote: > >> Hello guys, I produced a system "protein + lipid membrane" using the >> online >> tool CHARMM-GUI. Since

Re: [gmx-users] Pdb2gmx melts molecules due to bad distances

On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote: Hello guys, I produced a system "protein + lipid membrane" using the online tool CHARMM-GUI. Since I need to use the Amber force field, I added the Lipids17 force field inside Gromacs. The implementation should work fine, since the conversion of

[gmx-users] Pdb2gmx melts molecules due to bad distances

Hello guys, I produced a system "protein + lipid membrane" using the online tool CHARMM-GUI. Since I need to use the Amber force field, I added the Lipids17 force field inside Gromacs. The implementation should work fine, since the conversion of an equilibrated structure produces a nice and

[gmx-users] pdb2gmx

Hello  I want to create a .gro and .top file from my protein that contains 379 aminoacids in it's .pdb file by using gromos96 54a7 force field: pdb2gmx -f protein.pdb -o protein.gro -water spce -ignh but when gro and topology files are created , I see that message: Start terminus GLY-12: GLY-NH3+

[gmx-users] pdb2gmx peptide nanotube

*Dear Gromacs users,* I am trying to simulate a peptide nanutube composed by 8 cyclics.When I execute pdb2gmx with the options -missing and -ter (selecting manually None), as I have seen in the Gromacs list, I get this error: pdb2gmx -f tube.pdb -ter -missing -ignh8 out of 8 lines of

Re: [gmx-users] pdb2gmx do not work for unstable conformations

Dear Mark Abraham, Thank you so much for debugging it for me. The strange word could only be seen under Unix environment. After using dos2unix, the problem finally solves! I totally forgot to always use dos2unix. Thanks a lot for reminding me again! Yours sincerely Cheng

Re: [gmx-users] pdb2gmx do not work for unstable conformations

Hi, Some of your PDB files are malformed, which you could see with the less tool, or probably anything else. The first line, containing N, leads with strange characters, which stops pdb2gmx recognizing that they start with "ATOM," since they don't. Then N are recognized as missing. Mark On Sat,

[gmx-users] pdb2gmx do not work for unstable conformations

Dear Gromacs,I have a protein PDB structure as well as its mutants PDB, predicted by Rosetta with different ddG. After running pdb2gmx, I found that the structures with lower ddG (more stable) all perform okay; while structures with higher ddG (less stable) got fatal error: Fatal error:

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] 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] 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

[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] pdb2gmx handle the dna structure containing potassium

On 5/10/17 4:16 AM, Changdong LIU wrote: Dear GROMACS users, I used pdb2gmx to generate topology file for the g_quadruplex DNA which constains 3 potassiums. If the 3 potassiums were deleted ,the pdb2gma successfully generated the topology file for DNA. But failed when the 3

Re: [gmx-users] pdb2gmx handle the dna structure containing potassium

Take a look at you pdb file. May be potassium atom is defined as HETATM in pdb. amber99sb-ildn ff has K in its ions.itp file. On Wed, May 10, 2017 at 1:46 PM, Changdong LIU wrote: > Dear GROMACS users, > > > I used pdb2gmx to generate topology file for the g_quadruplex DNA which >

[gmx-users] pdb2gmx handle the dna structure containing potassium

Dear GROMACS users, I used pdb2gmx to generate topology file for the g_quadruplex DNA which constains 3 potassiums. If the 3 potassiums were deleted ,the pdb2gma successfully generated the topology file for DNA. But failed when the 3 potassiums were added into the pdb file. The topol.top

Re: [gmx-users] Pdb2gmx

Dear Lamm, It is GROMACS-5.0.7. So you need to use "gmx pdb2gmx" command. Best Wishes, Saumyak On 31 March 2017 at 11:55, Lamm Gro wrote: > Dear Gromacs users , > > I have installed Gromacs by this way : > http://www.gromacs.org/Documentation/Installation_ >

[gmx-users] Pdb2gmx

Dear Gromacs users , I have installed Gromacs by this way : http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation every thing was fine and I could install the package completely . But now I can't find pdb2gmx command ! Can you please let me know what

Re: [gmx-users] pdb2gmx generates very large .top for lipids with charmm36-nov2016.ff

So I found out why I didn't use charmm-gui initially, when using the protein membrane builder it removes the ligand minocycline. I have found a solution, on the unlikely chance what I have done will help someone, I'm going to post what I did. Since I used transformations on the protein (aligning

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

On 3/13/17 1:48 PM, Davit Hakobyan wrote: Just a small note about cholesterol CHL1 in the merged.rtp file of november 2016 release for CHARMM36 force field. The first four lines of CHL1 in merged.rtp: C3 CRL10.140 0 O3 OHL -0.660 1 H3' HOL0.430 2 H3

Re: [gmx-users] pdb2gmx generates very large .top for lipids with charmm36-nov2016.ff

I honestly forgot why (took too long, erred, or both) so I tried to do charm-gui again. From my current attempt it is taking a while. I'm on the last step and I'll keep checking the output. I'll keep you updated when something happens. Thanks again, your help is invaluable! - Jonathan P.S. I

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

Just a small note about cholesterol CHL1 in the merged.rtp file of november 2016 release for CHARMM36 force field. The first four lines of CHL1 in merged.rtp: C3 CRL10.140 0 O3 OHL -0.660 1 H3' HOL0.430 2 H3 HGA10.090 3 While the sequence

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

Thank you very much! Indeed, it seems the problem was in the missing TER lines in combination with -chainsep for individual chain separation. Thank you again for all your kind help. Davit On 3/13/2017 6:21 PM, Justin Lemkul wrote: On 3/13/17 1:12 PM, Davit Hakobyan wrote: Thank you for

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

Thank you. I have put the ZIP of the PDB file here: https://uni-muenster.sciebo.de/index.php/s/hO1OwfWMwwOy7xe The encountered error with the ASP residue relates to the C-terminal patch of the ANAA molecule which pdb2gmx missed and treating it as an unpatched ASP would give, of course, a

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

On 3/13/17 1:12 PM, Davit Hakobyan wrote: Thank you for the suggestion. I have tried to use the "-ter" flagbut this does not helpsince the problem is not because pdb2gmx cannot recognize the C-terminal patch, but that it misses the termianals of the intermediate proteins.The protein sequence

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

Hi, Using -ter to specify where molecules end won't help if there are not any TER records, but I can't tell what's in your file :-) Mark On Mon, Mar 13, 2017 at 6:12 PM Davit Hakobyan wrote: > Thank you for the suggestion. > > I have tried to use the "-ter" flagbut

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

Thank you for the suggestion. I have tried to use the "-ter" flagbut this does not helpsince the problem is not because pdb2gmx cannot recognize the C-terminal patch, but that it misses the termianals of the intermediate proteins.The protein sequence in my system is like:

Re: [gmx-users] pdb2gmx fails on CHARMM36 terminal group

Hi, pdb2gmx has options that configure its behaviour to let you choose whether PDB TER records and/or changes of chain ID should separate molecules, etc. You could explore those, and/or perhaps add such TER records to make your intent clearer to the tool. (But with incomplete information, I can't

Re: [gmx-users] pdb2gmx generates very large .top for lipids with charmm36-nov2016.ff

On 3/12/17 8:36 PM, Jonathan Saboury wrote: Hello all, I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the minimization, equilibration, and production runs given. Then I copied the 10ns production run .gro to a different folder so that I can run it with charmm36-nov2016.ff instead of

[gmx-users] pdb2gmx generates very large .top for lipids with charmm36-nov2016.ff

Hello all, I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the minimization, equilibration, and production runs given. Then I copied the 10ns production run .gro to a different folder so that I can run it with charmm36-nov2016.ff instead of the ff given. When running the command

Re: [gmx-users] pdb2gmx throws a fatal error for Carbon Monoxide

Thank you so much! It worked! Really appreciate the quick reply. Acqualine Lobo -- 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] pdb2gmx throws a fatal error for Carbon Monoxide

On 3/2/17 9:18 AM, Acqualine Lobo wrote: Thanks for the quick reply Dr. Justin! I did follow what you mentioned, however I still get the same error. I also tried changing the residue name in the pdb file to match the atom type as in the .atp file, the error still remains only with a different

Re: [gmx-users] pdb2gmx throws a fatal error for Carbon Monoxide

Thanks for the quick reply Dr. Justin! I did follow what you mentioned, however I still get the same error. I also tried changing the residue name in the pdb file to match the atom type as in the .atp file, the error still remains only with a different residue name. Instead of "Residue 'CMO' not

Re: [gmx-users] pdb2gmx throws a fatal error for Carbon Monoxide

On 3/1/17 7:29 AM, Acqualine Lobo wrote: Hello, I am trying to simulate a hemoglobin molecule in complex with CO. However, pdb2gmx throws a fatal error saying Fatal error: Residue 'CMO' not found in residue topology database For more information and tips for troubleshooting, please check the

Re: [gmx-users] PDB2GMX Fatal Error

>>> Use -ignh in pdb2gmx. >> Hi Reza, >> >> I tried -ignh, it's working fine. >> >> But i need to calculate H-bonds after docking the same peptide. Then >> the same error will crop up and I won't be able to calculate H-bonds. >> > > The use of -ignh has nothing to do with whether or not you can

[gmx-users] pdb2gmx throws a fatal error for Carbon Monoxide

Hello, I am trying to simulate a hemoglobin molecule in complex with CO. However, pdb2gmx throws a fatal error saying Fatal error: Residue 'CMO' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at

Re: [gmx-users] PDB2GMX Fatal Error

On 3/1/17 3:23 AM, Syed Azeem wrote: Use -ignh in pdb2gmx. Hi Reza, I tried -ignh, it's working fine. But i need to calculate H-bonds after docking the same peptide. Then the same error will crop up and I won't be able to calculate H-bonds. The use of -ignh has nothing to do with

Re: [gmx-users] PDB2GMX Fatal Error

> > Use -ignh in pdb2gmx. Hi Reza, I tried -ignh, it's working fine. But i need to calculate H-bonds after docking the same peptide. Then the same error will crop up and I won't be able to calculate H-bonds. >> On Mar 1, 2017, at 10:22, Syed Azeem wrote: >> >> Hi

Re: [gmx-users] PDB2GMX Fatal Error

Use -ignh in pdb2gmx. > On Mar 1, 2017, at 10:22, Syed Azeem wrote: > > Hi all, > > I tried passing a predicted peptide (16-mer) into GMX and ended up > with a fatal error regarding hydrogen. I tried ignoring the hydrogens > using -ignh command. But I'll need to

[gmx-users] PDB2GMX Fatal Error

Hi all, I tried passing a predicted peptide (16-mer) into GMX and ended up with a fatal error regarding hydrogen. I tried ignoring the hydrogens using -ignh command. But I'll need to calculate H-bonds for the next analysis, as I'll dock this peptide into a target protein. Fatal error: Atom HB3

Re: [gmx-users] pdb2gmx vsites error reading atom name

day, December 6, 2016 3:29:19 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] pdb2gmx vsites error reading atom name Hello I was wondering if someone has any idee as to what is happening with my .gro file.These are the first 3 atoms in my .gro file 1URE10C1 0.570

[gmx-users] pdb2gmx vsites error reading atom name

Hello I was wondering if someone has any idee as to what is happening with my .gro file.These are the first 3 atoms in my .gro file     1URE    10C    1   0.570   0.517   0.272     1URE    11C    2   0.555   0.365   0.285     1URE    12C    3   0.505   0.592   0.388now these are the first 3

[gmx-users] pdb2gmx and cyclic molecules

HI, Rebeca. The dangling bonds are due to inappropriate selection of terminals. You need to make lots of changes in respective files to get a gro for cyclic peptide.If your using charmm ff better try with the server. -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search

Re: [gmx-users] pdb2gmx

2016 15:30:14 -0400 From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx Message-ID: <d8bcd9d8-b628-8e61-70e6-42e2dcca9...@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.er

Re: [gmx-users] pdb2gmx

; >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] pdb2gmx >> Message-ID: <d8bcd9d8-b628-8e61-70e6-42e2dcca9...@vt.edu> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> >> >> On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.e

Re: [gmx-users] pdb2gmx

On 8/19/16 10:52 AM, amitbe...@chemeng.iisc.ernet.in wrote: Hello users, I am using pdb2gmx on a protein. Fatal error: Residue 1 named LYS 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

Re: [gmx-users] pdb2gmx

You need to check the archive or Google : Residue 1 named LYS 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 You might need to change the naming of your atoms according the forcefield your using

[gmx-users] pdb2gmx

Hello users, I am using pdb2gmx on a protein. Fatal error: Residue 1 named LYS 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 fixed. ATOM 1

Re: [gmx-users] pdb2gmx error

Hi, Why is your residue numbering and residue naming changing in mutually inconsistent ways? Mark On Thu, Jun 16, 2016 at 9:36 AM bharat gupta wrote: > Hi, > > I have been trying to build the toplogy for cellopentoase using the newly > derived parameters mentioned in

Re: [gmx-users] pdb2gmx error

Hi, I have been trying to build the toplogy for cellopentoase using the newly derived parameters mentioned in this paper: http://www.ncbi.nlm.nih.gov/pubmed/21387332. I got the paper from the gromacs website: http://www.gromacs.org/@api/deki/files/200/=56a_CARBO4GROMACS.rar When I try to

Re: [gmx-users] pdb2gmx error after switching force fields

On 5/13/16 11:04 AM, Irem Altan wrote: Hi, Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually using Gromacs 5.1.2. Not sure how that's possible. It should have been fixed prior to the release of 5.1.1. -Justin Best, Irem On May 13, 2016, at 10:52 AM,

Re: [gmx-users] pdb2gmx error after switching force fields

Hi, Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually using Gromacs 5.1.2. Best, Irem > On May 13, 2016, at 10:52 AM, Justin Lemkul wrote: > > > > On 5/13/16 10:49 AM, Irem Altan wrote: >> Hi, >> >> I have a .pdb file that I’ve used in

Re: [gmx-users] pdb2gmx error after switching force fields

On 5/13/16 10:49 AM, Irem Altan wrote: Hi, I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning: WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped to an

[gmx-users] pdb2gmx error after switching force fields

Hi, I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning: WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom

Re: [gmx-users] pdb2gmx -ignh

On 5/4/16 5:02 AM, Alexander Alexander wrote: Dear GMX user, As you know, naming the Hydrogen atom differently in different FF and in .pdb or .gro file brings lots of problems in the "gmx pdb2gmx". I also met the issue when I wanted to convert my self-made (by Avogadro) heptapeptide.pdb to

[gmx-users] pdb2gmx -ignh

Dear GMX user, As you know, naming the Hydrogen atom differently in different FF and in .pdb or .gro file brings lots of problems in the "gmx pdb2gmx". I also met the issue when I wanted to convert my self-made (by Avogadro) heptapeptide.pdb to heptapeptide.gro file. I could get rid of them

Re: [gmx-users] pdb2gmx assign CSER to non-terminal serine

Thank you Justin!!! That's the problem. Now everything runs well. Ruan On Tue, May 3, 2016 at 12:04 PM, Justin Lemkul wrote: > > > On 5/3/16 12:02 PM, Zheng Ruan wrote: > >> Hi Gromacs Users, >> >> I'm using pdb2gmx to process my pdb files with a phospho-tyrosine >> using

Re: [gmx-users] pdb2gmx assign CSER to non-terminal serine

On 5/3/16 12:02 PM, Zheng Ruan wrote: Hi Gromacs Users, I'm using pdb2gmx to process my pdb files with a phospho-tyrosine using amber99sb-ildn.ff. The relavant content in my pdb looks like this (There is a serine before phosphorylated tyrosine): ATOM202 N SER26 31.593 -68.669

[gmx-users] pdb2gmx assign CSER to non-terminal serine

Hi Gromacs Users, I'm using pdb2gmx to process my pdb files with a phospho-tyrosine using amber99sb-ildn.ff. The relavant content in my pdb looks like this (There is a serine before phosphorylated tyrosine): ATOM202 N SER26 31.593 -68.669 -25.834 1.00208.96 N ATOM203 CA

[gmx-users] pdb2gmx parametrization of proteins consisted of metallo-bindings cofactor sites

Dear Gromacs users! I am interesting what full atomistic force field integrated in the current GMX is better to use for the pdb2gmx parametrization of the HEME containing proteins like cytochrome C (where cofactor is not covalently bound to the polypeptide chain). e.g -ff amber 99sb did not

Re: [gmx-users] pdb2gmx disulfide bond in dimer

On 4/14/16 9:53 AM, s.varriale wrote: thank you Justin, but I can't understand how to solve my problem. when pdb2gmx links the 2 CYS, the resulting .gro file shows a unique chain because N- and C- termini of 2 chains are linked. As it should. The two chains have to be merged into a

Re: [gmx-users] pdb2gmx disulfide bond in dimer

thank you Justin, but I can't understand how to solve my problem. when pdb2gmx links the 2 CYS, the resulting .gro file shows a unique chain because N- and C- termini of 2 chains are linked. Sonia Il 14/04/2016 13:46 Justin Lemkul ha scritto: On 4/14/16 6:32 AM, s.varriale wrote: Dear

Re: [gmx-users] pdb2gmx disulfide bond in dimer

On 4/14/16 6:32 AM, s.varriale wrote: Dear all, I try to perform a MD simulation of a covalent dimer with gromacs 4.5.4. I do: pdb2gmx -f prot.pdb -chainsep ter and the programme generates a .gro file with disulfide bond. but when i want to minimize the system, there is an error: There were

[gmx-users] pdb2gmx disulfide bond in dimer

Dear all, I try to perform a MD simulation of a covalent dimer with gromacs 4.5.4. I do: pdb2gmx -f prot.pdb -chainsep ter and the programme generates a .gro file with disulfide bond. but when i want to minimize the system, there is an error: There were 2 inconsistent shifts. Check your

Re: [gmx-users] pdb2gmx error

Indeed Justin I have tried to add the entries for the capped groups in the Amber99SB-ILDN force field (like in the charmm*.ff) since they are not present in aminoacids.n.tdb and aminoacids.c.tdb, so I think I have broken something Stéphane On 4/5/16 6:47 AM, ABEL Stephane 175950

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