On 1/29/13 9:17 AM, amna khan wrote:
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 -ignh option will probably not work if the atom name is preceded by an
apostrophe (') as you have here. It appears your input .pdb file has some
nonstandard naming. If the atom was named H5, it would be ignored, but 'H5 is
not detected as being a hydrogen.
the error with charm and amber forcefiled are same
*
how to reomve this error for groamcs 43a1 or amber or chrm forcefield
Residues are named differently in each force field. For instance, in the Gromos
force fields, the names are DADE, DGUA, etc. Thus the coordinate file must
match the expectations of the force field (which is true for all force fields).
AMBER and CHARMM should work out of the box, and are far better options for
doing nucleic acid simulations than Gromos.
-Justin
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>
==============================**==========
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========================================
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
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