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

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

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

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.

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

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

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, > > >

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

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

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

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

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,

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

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 >

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_ >

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

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

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

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

Maybe you are trying to simulate a molecule that is not mentioned in the aminoacids.rtp on the force field of your choice or more probably the atom that is mentioned on the error report has a different name than the the one provided on the pdb file. My advice is to check on the ff directory >

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

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

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

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

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

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

Re: [gmx-users] pdb2gmx error

On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote: Hello, When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force field, I have the error : Fatal error: tpA = 53191, i= 0 in print_atoms I have no idea what does this message mean. Could you help me? This shouldn't

Re: [gmx-users] pdb2gmx & terminal residues

On 3/31/16 10:41 AM, Brett wrote: Dear Justin and All, The full screen output was as following and I am looking forward to getting a reply from you. gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

Re: [gmx-users] pdb2gmx & terminal residues

Dear Justin and All, The full screen output was as following and I am looking forward to getting a reply from you. gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-: GROMACS is written by:

Re: [gmx-users] pdb2gmx & terminal residues

On 3/31/16 8:18 AM, Brett wrote: Dear Justin and All, For terminal residue, regardless I select 0, 1, 2, the error messages always exist. I have opened the pdb by swiss deep view and resaved it, the same error message still exist. However if I choose force field 6: AMBER99SB-ILDN

Re: [gmx-users] pdb2gmx & terminal residues

Dear Justin and All, For terminal residue, regardless I select 0, 1, 2, the error messages always exist. I have opened the pdb by swiss deep view and resaved it, the same error message still exist. However if I choose force field 6: AMBER99SB-ILDN protein, the error message disappear. Will

Re: [gmx-users] pdb2gmx & terminal residues

On 3/30/16 10:41 PM, Brett wrote: Dear All, When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro -ignh" with force field, it gave me the warning as following, "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database,

Re: [gmx-users] pdb2gmx generate .itp file for each molecule

On 2/23/16 10:31 PM, Ray Chao wrote: ​Hi, gmx users, I used materials studio to generate a .pdb file containing 160 PTFE chains, and then modified the oplsaa forcefiled as Justin did. The pdb2gmx generated right .gro and .top files. But the problem is that it generated one .itp file for each

Re: [gmx-users] pdb2gmx generate .itp file for each molecule

Hi , Maybe you can try -merge all when using pdb2gmx. -- 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 (un)subscribe requests visit

Re: [gmx-users] pdb2gmx with GROMOS

That's good to know. Thanks for the clarifications. On 19 February 2016 at 14:22, Justin Lemkul wrote: > > It's because the GROMOS force fields are the only ones that explicitly > list [angles] in the .rtp file. All other force fields let these be > generated automatically by

Re: [gmx-users] pdb2gmx with GROMOS

It's because the GROMOS force fields are the only ones that explicitly list [angles] in the .rtp file. All other force fields let these be generated automatically by the bonded structure; this is due to some subtle ways in which the force field files differ in their organization (use of

Re: [gmx-users] pdb2gmx with GROMOS

Sure. I pasted my original mail at the bottom. I also followed your suggestion of trying the gromacs-master ff files, with identical results. What I'm trying to find out is why the warning is being triggered and if it's affecting the output in any way. My input is the 1AKI pdb file as downloaded

Re: [gmx-users] pdb2gmx with GROMOS

Can you remind me of the context here? You've provided output files that indicate everything is fine. If there's a problem with *input* please provide those files, the exact command and selections, etc. I recall there was some terminus issue, but I've replied to a few hundred posts since

Re: [gmx-users] pdb2gmx illegal instruction (core dumped)

Thank you David van der Spoel. I compile gromacs in my own laptop and I run on the same machine. Your guideline working properly. I reinstall gromacs and now all okk.. regards and thank you. Md Imrul Reza Shishir On Jan 28, 2016 4:47 PM, "David van der Spoel" wrote: > On

Re: [gmx-users] pdb2gmx illegal instruction (core dumped)

On 28/01/16 08:33, Md. Imrul Reza Shishir wrote: Hi Everyone. I use Lenovo A6-7310 (4 core 2MB cache memory) processor in my laptop. I install Gromacs 5.0.7 with latest cmake-3.4.2 and fftw-3.3.4. I use below Cmake command to install. "cmake .. -DGMX_BUILD_OWN_FFTW=ON

Re: [gmx-users] pdb2gmx with GROMOS

On 1/20/16 3:48 AM, Dries Van Rompaey wrote: Hi Justin and Marco, Thanks for your reply. I get this behaviour when I specify the default NH3+ and COO- termini through -ter, as well as when I don't use the -ter flag. Selecting the COOH terminus type removed the warning for the C-terminus, but

Re: [gmx-users] pdb2gmx, chain and segment names in the output pdb

Maxim Igaev писал 13-01-2016 19:51: Dear Gromacs users, I have a large molecular complex consisting of many identical monomers. I constructed a pdb file for it using VMD and assigned each monomer a segment name (A0, A1, A2 etc.). The chain name was however always the same - A. Then I created

Re: [gmx-users] pdb2gmx with GROMOS

Hi Justin and Marco, Thanks for your reply. I get this behaviour when I specify the default NH3+ and COO- termini through -ter, as well as when I don't use the -ter flag. Selecting the COOH terminus type removed the warning for the C-terminus, but selecting the NH2 terminus type did't remove the

Re: [gmx-users] pdb2gmx with GROMOS

On 1/19/16 10:26 AM, Dries Van Rompaey wrote: Dear gmx-users, I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx -f 1AKI.pdb), selecting any of the GROMOS force fields; all others work fine. I get the same error with the -ignh flag. WARNING: WARNING: Residue 1 named

Re: [gmx-users] pdb2gmx with GROMOS

You can try to add the -ter flag to pdb2gmx and manually select the n and c ter. Best, Marco Marco FRANZOI PhD Student University of Padua Department of biology, V floor South Tel: 3405086908 Mail: marco.franzo...@gmail.com On Tue, Jan 19, 2016 at 4:26 PM, Dries Van Rompaey <

Re: [gmx-users] pdb2gmx, chain and segment names in the output pdb

Hi, Unfortunately, pdb2gmx is only aware of chain ids, so you will not be able to preserve segment id. If the atom ordering is unchanged then you don't need the resulting PDB file, ie can use the original one. If not, then it's straightforward to use some scripting tool to re-unite your segment

Re: [gmx-users] pdb2gmx (ver 5.0.7) - choosing -ter "None" does not work

I have had this problem and I suspect that the answer lies in the Fatal error you receive. Grimace will not allow you to have dangling bonds. Something has to be attached to the first and last bond, otherwise it is not a viable molecule. Peter Sent from my iPad > On 2 בדצמ׳ 2015, at 18:03,

Re: [gmx-users] pdb2gmx error

On 10/15/15 4:18 AM, Dries Van Rompaey wrote: I did some more testing, it seems that this only occurs when the PRO residue is preceded by a glycine. Could this be related to this issue: http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I change the glycine residue to

Re: [gmx-users] pdb2gmx error

I did some more testing, it seems that this only occurs when the PRO residue is preceded by a glycine. Could this be related to this issue: http://comments.gmane.org/gmane.science.biology.gromacs.user/72687 ? When I change the glycine residue to anything else, pdb2gmx works like a charm. I

Re: [gmx-users] pdb2gmx error

On 10/8/15 1:54 AM, Dries Van Rompaey wrote: Thanks for the reply Justin. I unfortunately cannot currently disclose the files that I'm working on. Based on the info presented, would you say that it's an issue with the force field definition or with the actual protein topology? I am not

Re: [gmx-users] pdb2gmx error

On 10/7/15 3:01 PM, Dries Van Rompaey wrote: Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play.

Re: [gmx-users] pdb2gmx error

Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: > > > On 10/7/15 3:01 PM, Dries Van Rompaey wrote: > >>

Re: [gmx-users] pdb2gmx error

On 10/7/15 5:03 PM, Dries Van Rompaey wrote: Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. Without access to all of the files you're looking at, the best I can do

Re: [gmx-users] pdb2gmx error

Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey wrote: > Hi everyone, > > I'm getting the following warning when I try to run pdb2gmx on my

Re: [gmx-users] pdb2gmx warning

On 7/26/15 6:55 AM, faride badalkhani wrote: Dear all, I am performing a simulation on a plymeric structure, and I can exwcute pdb2gmx command successfully but there are some warnings as follows: Warning: Starting residue AMC1 in chain not identified as Protein/RNA/DNA. Warning: Starting

Re: [gmx-users] pdb2gmx error

On 7/26/15 6:46 AM, faride badalkhani wrote: Dear all, could anybody help me at this error? Fatal error: atom N not found in buiding block 1AMC while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at

Re: [gmx-users] pdb2gmx error residue not found in residue topology database

...@maillist.sys.kth.se] On Behalf Of su Sent: Wednesday, July 08, 2015 11:26 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx error residue not found in residue topology database How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co

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