Janowicz, Adrianna C. wrote:
Im sorry for the confusion.
I used an .itp file from the UCalgary site for dpc, I input a line
[ molecules ]
; molecule name nr.
DPC 65
SOL 6305
in the dpc.top file.
However, I generated the .gro file directly from the m65.pdb file from the
UCalgary site using the editconf command.
WARNING 1 [file dpc.top, line 28]:
18915 non-matching atom names
atom names from dpc.top will be used <=(taken from 1 dpc.itp x 65)
atom names from dpc.gro will be ignore <=(made from 65 dpc molecule pdb)
I replicated the error. The original coordinate file names its water hydrogens
as HW2 and HW3 rather than HW1 and HW2, as expected by most common water models.
It is safe to ignore this error.
-Justin
On Mon, July 25, 2011 8:21 am, Justin A. Lemkul wrote:
Janowicz, Adrianna C. wrote:
I used your tutorial but am getting the error message
WARNING 1 [file dpc.top, line 28]:
18915 non-matching atom names
atom names from dpc.top will be used
atom names from dpc.gro will be ignore
probably because my .top file was generated using a file generated thru
PRODRG (only inputing 23 DPC molecules and then specifying 65 of those
units) while the .gro file was created using the whole .pdb file of the
micelle containing all 65 units. How can I fix this error? -maxwarn 1
doesn't seem to be doing the trick.
I don't completely understand what you've done. PRODRG uses a single
molecule
to produce a topology that can then be #included in the system topology.
I
don't know how you inputted 23 molecules and then specified 65. What does
this
mean?
Also note that PRODRG topologies are usually insufficiently accurate for
actual
use in simulations:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
The source of the error could be one of several problems, please see:
http://www.gromacs.org/Documentation/Errors#XXX_non-matching_atom_names
-Justin
--
========================================
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
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--
========================================
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
========================================
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