Re: [gmx-users] Re: dangling bond at at one of the terminal ends

2012-06-04 Thread Justin A. Lemkul
On 6/4/12 7:29 AM, ramaraju801 wrote: 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. Then you'll have to translate this newfound knowledge int

[gmx-users] Re: dangling bond at at one of the terminal ends

2012-06-04 Thread ramaraju801
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-o

Re: [gmx-users] Re: dangling bond at at one of the terminal ends

2012-06-03 Thread Thomas Piggot
Hi, You may also need to name your terminal DNA residues appropriately in your pdb file, as for the AMBER force fields the terminal DNA residues are named differently. Check out the dna.rtp file for these naming conventions. Cheers Tom On 03/06/12 14:50, Justin A. Lemkul wrote: On 6/3/1

[gmx-users] Re: dangling bond at at one of the terminal ends

2012-06-03 Thread ramaraju801
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 l

Re: [gmx-users] Re: dangling bond at at one of the terminal ends

2012-06-03 Thread Justin A. Lemkul
On 6/3/12 9:47 AM, ramaraju801 wrote: 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 amber9

[gmx-users] Re: dangling bond at at one of the terminal ends

2012-06-03 Thread ramaraju801
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

[gmx-users] Re: dangling bond at at one of the terminal ends

2012-05-30 Thread ramaraju801
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 startin