hi, i want to simulate the DNA with gormacs forcefield, accrding to literatre Charm and amber are best to be used but GROMACS96 43A1 force field can be also used
the error with GROMACS96 43A1 is *Fatal error:* *Residue 'DA' not found in residue topology database* this is same error with gromacs 43a2. gromacs 45 3a, gromacs 53a5, gromacs 53 a6 and opls/a [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges [DEPRECATED] Gromacs force field (see manual) [DEPRECATED] Gromacs force field with hydrogens for N with charm force field is *Fatal error:* *Atom H7 in residue DA 1 was not found in rtp entry DA with 30 atoms* *while sorting atoms.* * * i have also use -ignh option, but stiill the problem comes which is as follows *Fatal error:* *Atom ''H5 in residue DA 1 was not found in rtp entry DA with 30 atoms* *while sorting ato*ms. for amber *Fatal error:* *Atom H7 in residue DA 1 was not found in rtp entry DA5 with 30 atoms* *while sorting atoms.* *and by -ignh command * * * * Fatal error: Atom ''H5 in residue DA 1 was not found in rtp entry DA5 with 30 atoms while sorting atoms. the error with charm and amber forcefiled are same * how to reomve this error for groamcs 43a1 or amber or chrm forcefield On Sat, Jan 26, 2013 at 6:13 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/26/13 4:18 AM, amna khan wrote: > >> hi, all , >> >> i want to simulate dna with ligand/drug >> >> i am getting error in generating he topology for dna . >> > > We can't help you unless you show us what the error is and provide (at the > very least) your exact pdb2gmx command. > > > I'm unable to do using the pdb2gmx with any of the force fields. Could >> anyone please tell if I can get any tutorial for the DNA-drug simulation. >> > > Exercise Google here. If it exists, you should be able to find it by > searching or visiting gromacs.org. > > > or which forcefield should i use ? >> >> > What does your analysis of the literature suggest would be the best choice? > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
