RE: [gmx-users] Regarding error.
Check this page for clarification http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group I guess this issue was also addressed before : http://lists.gromacs.org/pipermail/gmx-users/2011-February/058868.html Cheers, EB From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Seera Suryanarayana Sent: Tuesday, 19 June 2012 4:50 PM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding error. Dear all gromacs users, While i am running the commond mdrun -deffnm nvt i am getting the following error. Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. Kindly tell me how to over come this error. Suryanarayana Seera, JRF, 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 error.
On 6/15/12 4:08 AM, Seera Suryanarayana wrote: Dear all gromacs users, While i am running the commond trjconv -f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500 i am getting the following warning. WARNING no output, last frame read at t=10 Kindly tell me how to overcome this error. The .trr file contains time frames only up to 10 ps, so you can't dump out a frame at 500 ps - it doesn't exist. -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
RE: [gmx-users] Regarding error
Have you incorrectly changed the numbers in the topology, the difference in the number is 8, so it appears your coordinate file contains 8 more atoms than the topology. You will have to work out how that is. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Seera Suryanarayana Sent: Friday, 8 June 2012 3:32 PM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding error Dear all gromacs users, While running the grompp commond after addition of counter ions i am getting the following error. Fatal error: number of coordinates in coordinate file (3ASW_ion.gro, 178301) does not match topology (3ASW.top, 178293) Here i am sending my .top file,kindly tell me how to overcome this error. ; ; File '3ASW.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Sat Jun 9 10:36:25 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f 3ASW.pdb -o 3ASW.gro -p 3ASW.top -missing ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp ; Include chain topologies #include 3ASW_Protein_chain_A.itp #include 3ASW_Protein_chain_B.itp ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp ;#include ions.itp [ system ] ; Name CLUMPING FACTOR B; TAIL REGION DERIVED PEPTIDE in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 129 SOL 5 SOL 58209 NA ions 8 /Add NA ions Suryanarayana Seera, JRF, 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 error.
There is no GROMACS tool that repairs incomplete structures, but you can find other programs that can do it. Some of them have been previously posted in this list (try a search on it). Personally I've used Swiss PDB viewer, which is useful to add missing atoms. Javier El 06/06/12 07:42, Seera Suryanarayana escribió: Dear all gromacs users, I have 1VZV.pdb file, in that file HIS231 has incomplete ring as N atom is missing.Can i add N atom to the .pdb file if possible how can i add that atom to .pdb file. Suryanarayana Seera, PhD student, 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 error.
I use MacroMolecular Builder for all sorts of things, including filling in missing atoms. Erik 6 jun 2012 kl. 08.59 skrev Javier Cerezo: There is no GROMACS tool that repairs incomplete structures, but you can find other programs that can do it. Some of them have been previously posted in this list (try a search on it). Personally I've used Swiss PDB viewer, which is useful to add missing atoms. Javier El 06/06/12 07:42, Seera Suryanarayana escribió: Dear all gromacs users, I have 1VZV.pdb file, in that file HIS231 has incomplete ring as N atom is missing.Can i add N atom to the .pdb file if possible how can i add that atom to .pdb file. Suryanarayana Seera, PhD student, 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 error.
It seems that redefinition comes from including tow different ions.itp files, here: ; Include topology for ions #include gromos43a1.ff/ions.itp #include ions.itp Javier El 06/06/12 10:51, Seera Suryanarayana escribió: Dear all gromacs users, After added the counter ions to the top file and further i used 'grompp' commond,i got the following error. Fatal error: moleculetype CU1 is redefined. This error occurs due the duplication of CU1 in .top file. But i cannot find that error in my .top file.Here i am sending my .top file. Kindly tell me how to overcome this error. ; ; File '1UZ9.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Thu Jun 7 13:55:15 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f 1UZ9.pdb -o 1UZ9.gro -p 1UZ9.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp ; Include chain topologies #include 1UZ9_Protein_chain_A.itp #include 1UZ9_Protein_chain_B.itp ; Include water topology #include gromos43a1.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp #include ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 13532 NA charge 3 /Add NA ions Thanks and regards Suryanarayana Seera, JRF, India. -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- 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 error
The error itself is self explanatory, there are no 22 atoms in your protein structure, that suppose to be there. If you want to ignore those atoms when you build your topology you can use the -missing option when you run pdb2gmx. But if you need all the atoms you better construct a complete protein structure using some other software before you run pdb2gmx. Cheers, = Emmanuel Birru PhD Candidate Faculty of Pharmacy and Pharmaceutical Sciences Monash University (Parkville Campus) 381 Royal Parade, Parkville Victoria 3052, Australia Tel: Int + 61 3 9903 9187 E-mail: emanuel.bi...@monash.edumailto:firstname.lastn...@monash.edu www.pharm.monash.edu.auhttp://www.pharm.monash.edu.au/ From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Seera Suryanarayana Sent: Monday, 4 June 2012 3:52 PM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding error Dear all gromacs users, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. 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 error
On 4/06/2012 5:05 PM, Seera Suryanarayana wrote: Dear all gromacs users, While i am running pdb2gmx commond i am getting following error. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. I wont ignore the 22 missing atoms by using -missing commond. I would like to construct a complete protein structure.But i dont know how to construct the complete protein sturcture.Kindly tell me how to consturct the complete protein and what are the softwares i have to use here. There is no general answer to this question. You have to examine the file, see what is missing, perhaps find out why, and then perhaps use various possible solutions. Some leads are here... http://www.gromacs.org/Documentation/File_Formats/Coordinate_File 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
RE: [gmx-users] Regarding error
I guess you have duplicate the moleculetype entries for CU1 in your topology file. Check your topology file again. You can not have more than one moleculetype definition per molecule type. Cheers, Emmanuel = Emmanuel Birru PhD Candidate Faculty of Pharmacy and Pharmaceutical Sciences Monash University (Parkville Campus) 381 Royal Parade, Parkville Victoria 3052, Australia Tel: Int + 61 3 9903 9187 E-mail: emanuel.bi...@monash.edumailto:firstname.lastn...@monash.edu www.pharm.monash.edu.auhttp://www.pharm.monash.edu.au/ From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Seera Suryanarayana Sent: Tuesday, 29 May 2012 5:02 PM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding error Dear all gromacs users, I tried the grompp -c 3I40_ion.gro -p 3I40.top -o 3I40_b4em.tpr -f em.mdp and i got the following error. Option Filename Type Description -f em.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 3I40_ion.gro InputStructure file: gro g96 pdb tpr etc. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc. -n index.ndx Input, Opt. Index file -p 3I40.top InputTopology file -pp processed.top Output, Opt. Topology file -o 3I40_b4em.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -[no]v bool no Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing. Not for normal use and may generate unstable systems -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.19# Generated 279 of the 1225 non-bonded parameter combinations --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1228 Fatal error: moleculetype CU1 is redefined. Is there any explanation why is thid happening? I would appreciate any help. Iam new in using MD and gromac 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 error
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Seera Suryanarayana [paluso...@gmail.com] Sent: Friday, May 25, 2012 6:23 AM To: gmx-users@gromacs.org Subject: [gmx-users] Regarding error Dear all gromacs users, While i am using the commond pdb2gmx -f 4E82.pdb -o 4E82.gro -p 4E82.top.I am getting the following warnings and errors. Warning: Residue EME21 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ILE22 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue SER23 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLY24 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ARG25 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue CYS20 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3CYS5 CYS10 CYS20 CYS30 SG18SG36SG75 SG144 SG228 CYS5SG36 0.834 CYS10SG75 0.936 1.000 CYS20 SG144 0.833 0.203 0.935 CYS30 SG228 0.856 0.827 0.200 0.788 CYS31 SG234 0.202 0.860 0.783 0.820 0.734 Linking CYS-3 SG-18 and CYS-31 SG-234... Linking CYS-5 SG-36 and CYS-20 SG-144... Linking CYS-10 SG-75 and CYS-30 SG-228... Start terminus ALA-1: NH3+ End terminus CYS-20: COO- Fatal error: Residue 'EME' not found in residue topology database. http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database Jan Kindly tell me how to over come this error. 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 error
On 5/25/12 1:23 AM, Seera Suryanarayana wrote: Dear all gromacs users, While i am using the commond pdb2gmx -f 4E82.pdb -o 4E82.gro -p 4E82.top.I am getting the following warnings and errors. Warning: Residue EME21 in chain has different type (Other) from starting residue ALA1 (Protein). Warning: Residue ILE22 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue SER23 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue GLY24 in chain has different type (Protein) from starting residue ALA1 (Protein). Warning: Residue ARG25 in chain has different type (Protein) from starting residue ALA1 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue CYS20 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3CYS5 CYS10 CYS20 CYS30 SG18SG36SG75 SG144 SG228 CYS5SG36 0.834 CYS10SG75 0.936 1.000 CYS20 SG144 0.833 0.203 0.935 CYS30 SG228 0.856 0.827 0.200 0.788 CYS31 SG234 0.202 0.860 0.783 0.820 0.734 Linking CYS-3 SG-18 and CYS-31 SG-234... Linking CYS-5 SG-36 and CYS-20 SG-144... Linking CYS-10 SG-75 and CYS-30 SG-228... Start terminus ALA-1: NH3+ End terminus CYS-20: COO- Fatal error: Residue 'EME' not found in residue topology database. Kindly tell me how to over come this error. Whenever you encounter an error, your first source of information should be http://www.gromacs.org/Documentation/Errors. This error, and most of the others you are likely to encounter, have been asked and answered hundreds (if not thousands) of times already. For instance: http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -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
Re: [gmx-users] Regarding error.
On Thu, May 24, 2012 at 10:20 AM, Seera Suryanarayana paluso...@gmail.comwrote: Dear all gromacs users, while running the command grompp -c 1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp i am getting the following error. File input/output error: pr.mdp Please tell me how to over come this error Hi Seera , the error is self explainable, you dont have pr.mdp in your working directory. Make pr.mdp as mention in tutorial With Best Wishes, Rama David -- 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 error.
On 5/22/12 2:00 PM, Seera Suryanarayana wrote: Dear all gromas users, While i am running the grompp -c 1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp 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. I answered this already: http://lists.gromacs.org/pipermail/gmx-users/2012-May/071679.html If something is still unclear, reply to that post and explain what you don't understand, otherwise it just seems as if you're ignoring advice you're being given. -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
Re: [gmx-users] Regarding error.
Hi Seera As the error message is telling you, the molecule type CU1 is defined more than once along your topology. Check it, locate the [ moleculetype ] sections and verify that CU1 is defined only once. If that does not solve the problem, you can post you topology here so that we can try to identify the source for the error. Javier El 21/05/12 10:55, Seera Suryanarayana escribió: Dear all gromacs users, I tried the grompp and i got the following error. Fatal error: moleculetype CU1 is redefined. Is there any explanation why is thid happening? I would appreciate any help. Iam new in using MD and gromac in particular. Suryanarayana Seera, PhD student, HYderabad, India. -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 -- 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 error.
Hi Suryanarayana, http://www.gromacs.org/Documentation/Errors is where i'd start. But to help you along this error suggests that you have a different number of atoms in your coordinate file(.gro) than your topology(.top) suggests. Often this can be caused by adding or removing ions or solvent without modifying your .top file. Regards, Dylan Smith On 2012-05-22 15:03, Seera Suryanarayana wrote: Dear all gromacs users, I tried the grompp and i got the following error. Fatal error: number of coordinates in coordinate file (1UZ9_ion.gro, 41103) does not match topology (1UZ9.top, 41100) Is there any explanation why is thid happening? I would appreciate any help. Iam new in using MD and gromac 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 error.
On Fri, May 18, 2012 at 12:20 PM, Seera Suryanarayana paluso...@gmail.comwrote: Dear all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Residue 'CSD' not found in residue topology database First read: http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Anirban 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 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 error.
On 18/05/2012 4:50 PM, Seera Suryanarayana wrote: Dear all, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: Residue 'CSD' not found in residue topology database Please search for your own answers before posting. You'll learn more and faster! This error, and most others, are discussed here: 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
Re: [gmx-users] Regarding error
On Mon, Apr 30, 2012 at 11:50 AM, seera suryanarayana paluso...@gmail.comwrote: Respected Sir, While i am running the gromacs software to simulate the protein i am getting the following error. Fatal error: Residue 'GNP' not found in residue topology database http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Anirban Suryanarayna 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
Re: [gmx-users] Regarding error in ion neutralization step
On 5/11/2011 1:05 AM, kirubakaran palani wrote: Dear All Could any one help me to solve this error in gromacs 4.5.5 version. I am running dynamics on apo protein and the protein shows negative charge of -6 (after choosing OPLS-AA force filed) and when i was neutralizing the -6 with +6 and generating the genion.tpr file there it shows No such moleculetype NA+ error. But the same protein was running with out any error message in gromacs 4.0.7 version. The naming convention has changed. See share/top/oplsa.ff/ions.itp Mark The error message was given below. Kindly rectify the problem === [student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o genem.tpr Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype NA+ For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Regards Kirubakaran P -- 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 error during genion step before energy minimization
Meenakshi wrote: Hi, I am doing MD simulation of protein-ligand system using G53a6 as forcefield. I got the ligand.itp file for ffG53a6 from the ATB (Automated Topology Builder) server. I included the ligand.itp in the .top file, generated an octahedron solvation box, solvated it and did the grompp step before energy minimization. It was fine so far. However, when I performed the genion step to neutralize the charge on the system, it threw an error: --- Program genion, VERSION 4.0.5 Source code file: ../../../../src/mdlib/ns.c, line: 2193 Fatal error: Max #atoms in a charge group: 33 32 --- My ligand has 33 atoms. While searching the mailing list for a solution to this problem I came across this link http://comments.gmane.org/gmane.science.biology.gromacs.devel/2846 I assume this is a bug in Gromacs 4.0.5. Has the bug been fixed? Please help me find a solution to this problem. IIRC, there have been changes to the maximum allowable size to a charge group, but instead of thinking of this problem as a bug, you should really consider the fact that no sensible charge group should ever have that many atoms, let alone encompass an entire molecule! You will have significant artifacts in nonbonded interaction calculations. Garbage in, garbage out as the saying goes. -Justin Thanks, Meenakshi Pradhan TCS Innovations Lab Tata Consultancy Services Ltd Madhapur, Hyderabad India mail: meenak...@atc.tcs.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] regarding error in editconf
Anamika Awasthi wrote: Dear friends when I am trying command editconf, it is showing error File input/output error I have protein of 700 amino acids and its of inverted T shape and we are giving boxtype dodecahedron. input command is: editconf_d -bt dodecahedron -f input.gro -o box.gro -c -d 10.0 If you're getting an I/O error, then either the input file doesn't exist or you don't have permission or sufficient disk space to write the output. The full error message probably would have given more clues, but the reason likely falls into one of these categories. -Justin with regards Anamika -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] Regarding Error Atomtype OS not found
On 13/04/2010 1:49 PM, Jignesh Patel wrote: Hello, while I am running grompp command, I am getting following error. Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 837 of the 2346 non-bonded parameter combinations --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 947 Fatal error: Atomtype OS not found Can anyone help me to solve this problem? Yep, they can point out that atom type OS is not found. Since at this stage only you know about your topology and system preparation, and more particularly why you're trying to #include ff_dum.itp, only you can reason why. Perhaps sharing some more detail will help... 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/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/mailing_lists/users.php
