Re: [gmx-users] Regarding errors.
On 5/22/12 1:26 PM, Seera Suryanarayana wrote: Dear all gromas users, While i am running the grompp after first mdrun command i got the following error. File input/output error: pr.mdp Is there any explanation why is this happening? It means that file doesn't exist in the working directory. I would appreciate any help.I am new in using MD and gromacs in particular. Do all the tutorials you can find until basic workflows become second nature. Here are a few: http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors.
Dear all gromas users, While i am running the grompp after first mdrun command i got the following error. File input/output error: pr.mdp Is there any explanation why is this happening? I would appreciate any help.I am new in using MD and gromacs in particular. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding errors.
On 18/05/2012 4:43 PM, Seera Suryanarayana wrote: Dear all, While i am running gromacs software i am getting following error.Let me know how to over come that error Fatal error: number of coordinates in coordinate file (208L_ion.gro, 62283) does not match topology (208L.top, 62293) The number of coordinates must match. See discussion of the [molecules] section in chapter 5 of the manual. That's probably what you should fix, probably with the number of solvent and ion atoms changing. genion -p will do this for you if you tell it to do so. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors.
Dear all, While i am running gromacs software i am getting following error.Let me know how to over come that error Fatal error: number of coordinates in coordinate file (208L_ion.gro, 62283) does not match topology (208L.top, 62293) Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Regarding errors
Dear Suryanarayana Seera Please check the itp files mentioned in the topol.top and what u used in your commands. Especially check the solvent model. May be you have not changed that in the topol.top file. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Seera Suryanarayana [paluso...@gmail.com] Sent: Monday, May 14, 2012 2:58 PM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding errors Dear all gromacs users, I tried the grompp and i got the following error."number of coordinates in coordinate file (4INS_b4ion.gro, 90396) does not match topology (4INS.top, 90393)". Is there any explanation why is this happens.I would appreceate any help.I am new in using moleculer dynamics and particularly in gromacs. Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. Regards Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors
Dear all gromacs users, I tried the grompp and i got the following error."number of coordinates in coordinate file (4INS_b4ion.gro, 90396) does not match topology (4INS.top, 90393)". Is there any explanation why is this happens.I would appreceate any help.I am new in using moleculer dynamics and particularly in gromacs. Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. Regards Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding errors
On Fri, Apr 27, 2012 at 3:17 PM, seera suryanarayana wrote: > Respected Sir, > > While i am running gromacs software i am getting the > following error.Kindly knowing me how to over come the error. > > Fatal error: > number of coordinates in coordinate > file (1cys_ion.gro, 99670) > does not match topology (1cys.top, > 99680) > > Your .top file contains 10 extra atoms than you .gro file. Check whether any ion has been mentioned twice by mistake in the .top file. > > > SURYANARAYANA SEERA, > PhD student. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors
Respected Sir, While i am running gromacs software i am getting the following error.Kindly knowing me how to over come the error. Fatal error: number of coordinates in coordinate file (1cys_ion.gro, 99670) does not match topology (1cys.top, 99680) SURYANARAYANA SEERA, PhD student. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding errors
On 27/04/2012 5:07 PM, seera suryanarayana wrote: Respected Sir, While i am running the gromacs software i am getting the following error.Kindly knowing how to over come the error. Fatal error: Residue 'CCN' not found in residue topology database http://www.gromacs.org/Documentation/Errors Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors
Respected Sir, While i am running the gromacs software i am getting the following error.Kindly knowing how to over come the error. Fatal error: Residue 'CCN' not found in residue topology database SURYANARAYANA SEERA, PhD student. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding errors
On 27/04/2012 3:53 PM, seera suryanarayana wrote: Respected sir, While i am running the gromacs software i am getting the following error.Kindly tell me how to over come the error. Fatal error: Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms while sorting atoms. Please check out http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette for advice on how to construct effective requests for help. With only the above information, all that can be said is that the tool you were using expected residue LYS that was first in some sequence, and that was being mapped to .rtp entry LYSH, to lack atom an atom named HA. Background information on the required matching can be found in chapter 5 of the manual. Details of how the mismatch occurred can only be found in the files you have constructed. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding errors
Respected sir, While i am running the gromacs software i am getting the following error.Kindly tell me how to over come the error. Fatal error: Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms while sorting atoms. SURYANARAYANA SEERA, PhD student -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
