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 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 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 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 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

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

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

I never did that. -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 su Sent: Wednesday, July 08, 2015 11:26 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx error residue

Re: [gmx-users] pdb2gmx error with addition of terminal group

On 7/8/15 6:39 AM, anu chandra wrote: Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have downloaded Gromacs compatible Chamrmm36ff from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the

Re: [gmx-users] pdb2gmx error

If I got it right I would suggest this. Try removing parts in your overall structure. For example let's say your system has 3 components water, ATP, TPO. Try removing all but water, try pdb2gmx, all but ATP ( like a sim in vacuo ) try once again pdb2gmx. This will make the troubled part

Re: [gmx-users] pdb2gmx error with addition of terminal group

Thanks Justin. Its working fine. On Wed, Jul 8, 2015 at 12:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/8/15 6:39 AM, anu chandra wrote: Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have

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

Look at the file: residuetypes.dat in the ../top/ directory of your installation. It lists all the residue names and more. Peter Stern Weizmann Institute Sent from my iPad On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd hamisu.kaza...@yahoo.com wrote: Dear gmx-users, I am really new in

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 ordinates. Sent from my iPhone On 08-Jul-2015, at 11:16 pm, Peter Stern peter.st...@weizmann.ac.il wrote: Look at the file: residuetypes.dat in the ../top/ directory of your

Re: [gmx-users] pdb2gmx error

On 4/7/15 7:53 AM, Sneha Menon wrote: Dear all, I want to simulate a polymer - triphenylphosphine connected to a polyethylene glycol polymer using the CHARMM36 forcefield. I obtained the parameters of this polymer (resname TPP) using SwissParam. I added this molecule to the forcefield by

Re: [gmx-users] pdb2gmx error

Hi, These errors mean exactly what they say. There's a mismatch between your structure file and the residue structure in the database. So you need to look at them both and see what is wrong. Chapter 5 of the manual is your friend. Mark On 19/03/2015 3:17 am, RJ ra...@kaist.ac.kr wrote: Dear