[gmx-users] Re: Fatal error: Atomtype O2 not found
hi sorry 4 not doing it before, right now am doing Solvate the Box step in molecular modelling am using Gromacs 4.5.5 ver during the first step i.e creating the topology file ,i tried to create the topology file by using the command pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.pdb –p fws.top for which gromacs showed me an error saying atomtypeXX not found in the residue type database i resolved this issue by going through gromacs manual by adding the missing atoms to the dna.rtp file and new atoms to atomtypes.atp file after which it produced the topology file int he next step i setup an box with the command editconf -bt cubic –f fws.pdb –o fws.pdb -c –d 0.9 in the third step i.e Solvate the Box i used the command genbox –cp fws.pdb –cs spc216.gro –o fws_b4em.pdb –p fws.top in the fourth step i.e Setup the energy minimization. i used the command grompp –f em.mdp –c fws_ion.pdb –p fws.top –o fws_em.tpr where its givving me an errror which says Fatal error: Unknown bond_atomtype O2 based on your replies i tried by adding the atom to ffbonded.itp file but it dint work. am attachning my dna.rtp ,atomtypes.atp,ffbonded .itp files please help -ram http://gromacs.5086.n6.nabble.com/file/n4998335/dna.rtp dna.rtp http://gromacs.5086.n6.nabble.com/file/n4998335/ffbonded.itp ffbonded.itp http://gromacs.5086.n6.nabble.com/file/n4998335/atomtypes.atp atomtypes.atp -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998335.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Fatal error: Atomtype O2 not found
hi am working on a DNA-protein complex, during the energy minimization step its giving the following error, Fatal error: Atomtype O2 not found am using charmm27 force field and used the command grompp -f minim.mdp -c protein.gro -p protein.top -o protein-EM-vacuum.tpr regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Fatal error: Atomtype O2 not found
yes, when creating the topology file i added atom O2 to the .rtp file when it said atom O2 is missing in atomstype regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998256.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Fatal error: Atomtype O2 not found
correction i added O2 atom to atomtypes.atp file regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998257.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Fatal error: Atomtype O2 not found
@ Mark, i added -ter to pdb2gmx command and produced the topology file but still the energy minimization step in vacuum is producing the same error @justin am presently running the simulation step i.e energy minimization of structure in vacuum. when producing the topology file ,it gave errors saying some of the atoms are missing in atomtypes which i gave , you said atoms shouldn't be added which were not in the first place then can u tell me the alternative. regards ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998261.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Fatal error: Atomtype O2 not found
as i said my system is an protein-DNA complex and the error popped up only for atoms in DNA residues. -ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998263.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: dangling bond at at one of the terminal ends
hi, i checked the .rtp file residues such as DCN,DC5,DGN,DG5,DAN,DA5,DTN,DT5 dint have any phosphate gp but when i tested the .rtp file with a random DNA pdb file it is producing a topology file. -ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-dangling-bond-at-at-one-of-the-terminal-ends-tp4998029p4998051.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: dangling bond at at one of the terminal ends
HI, everyone am working on a system consisting of protein-DNA complex,where an protein comes and binds to the DNA to form a complex. To produce an topology file in gromacs i gave the command pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter -ignh -ff amber99 . its creating the topology files of the protein but when its starts creating the topology file for the DNA seq its recognizing the starting and the ending terminus residue. and then stops giving an error Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried editing the .n.tdb and .c.tbd files by writing the terminal residues of DNA in those files but then its giving an error which says need an directive before the residue must been and old file plz help, regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-dangling-bond-at-at-one-of-the-terminal-ends-tp4998029.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: dangling bond at at one of the terminal ends
there were two atoms that were new , i provided them in the .rtp file. only then i ran the command regards ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-dangling-bond-at-at-one-of-the-terminal-ends-tp4998029p4998031.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file.
when i ran gromacs to produce topology file for a nucleotide sequence it is showing the above error saying There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried giving the starting and ending residues in .n.tdb and .c.tdb files but it did not work with an error saying Fatal error: reading termini database: directive expected before line: P am uploading my PDB file of my DNA-protein compex sequence in which the nucleotide sequence ranges from 1 to 12216 http://gromacs.5086.n6.nabble.com/file/n4997922/dnaseq_rot1.pdb dnaseq_rot1.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/dangling-bond-at-at-least-one-of-the-terminal-ends-and-the-force-field-does-not-provide-terminal-ent-tp4997922.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] angling bond at at one of the terminal ends
hi, recently while working on gromacs i came across this error There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried to edit .tdb file by giving the terminal entries but its not working.. plz help me out regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/angling-bond-at-at-one-of-the-terminal-ends-tp4997894.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: dangling bond at at one of the terminal ends
my fault, when i ran gromacs to produce topology file for a nucleotide sequence it is showing the above error There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried giving the starting and ending residues in .n.tdb and .c.tdb files but it did not work with an error saying Fatal error: reading termini database: directive expected before line: P am uploading my PDB file of my DNA-protein compex sequence in which the nucleotide sequence ranges from 1 to 12216 http://gromacs.5086.n6.nabble.com/file/n4997914/dnaseq_rot1.pdb dnaseq_rot1.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/angling-bond-at-at-one-of-the-terminal-ends-tp4997894p4997914.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
