Janowicz, Adrianna C. wrote:
thanks! one last problem:
Im using the dpc.itp file & I keep getting an error having a problem with
the 0 mass for the atoms 11-23 (I've searched forums & haven't found
anyone having a problem with the 0 masses), along with No default Proper
Dih. types, No default Bond types No default Ryckaert-Bell. types & No
default LJ-14 types!!
These errors come up all the time, I'm surprised you haven't found the answers
in the archive.
With respect to the zero masses, it's because the [atoms] section does not list
masses, so they're set to zero. The proper format would have mass listed in the
column to the right of charge. The reason it's missing is because the topology
posted online is for (1) an ancient version of Gromacs (probably in the 3.x
series) and (2) for use with the deprecated ffgmx force field, which had some
different internal mechanics. Note that this is not a reason to use ffgmx
(please refer to the manual for the full explanation as to why you shouldn't use
it).
The missing parameters are also probably due to similar issues. I believe you
said you were using my tutorial as a basis for your simulations, so you'll have
to make all the parameters conform to the 53a6 nomenclature. For instance, atom
type OS was replaced by either OE or OA, depending on the functional group.
You'll have to update the topology accordingly. There are probably other such
issues, as well.
-Justin
DPC.itp from UCalgary site:
1 CH3 1 DPC C1 1 0.4 ; qtot: 0.248
2 CH3 1 DPC C2 1 0.4 ; qtot: 0.496
3 CH3 1 DPC C3 1 0.4 ; qtot: 0.744
4 NL 1 DPC N4 1 -0.5 ; qtot: 0.752
5 CH2 1 DPC C5 1 0.3 ; qtot: 1
6 CH2 1 DPC C6 1 0.4 ; qtot: 1
7 LOS 1 DPC O7 1 -0.8 ; qtot: 0.64
8 P 1 DPC P8 1 1.7 ; qtot: 1.64
9 OM 1 DPC O9 1 -0.8 ; qtot: 1
10 OM 1 DPC O10 1 -0.8 ; qtot: 0.36
11 LOS 1 DPC O11 1 -0.7 ; qtot: 0
12 CH2 1 DPC C12 5 0 ; qtot: 0
13 CH2 1 DPC C13 6 0 ; qtot: 0
14 CH2 1 DPC C14 7 0 ; qtot: 0
15 CH2 1 DPC C15 8 0 ; qtot: 0
16 CH2 1 DPC C16 9 0 ; qtot: 0
17 CH2 1 DPC C17 10 0 ; qtot: 0
18 CH2 1 DPC C18 11 0 ; qtot: 0
19 CH2 1 DPC C19 12 0 ; qtot: 0
20 CH2 1 DPC C20 13 0 ; qtot: 0
21 CH2 1 DPC C21 14 0 ; qtot: 0
22 CH2 1 DPC C22 15 0 ; qtot: 0
23 CH3 1 DPC C23 16 0 ; qtot: 0
On Tue, July 26, 2011 1:16 pm, Justin A. Lemkul wrote:
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
========================================
--
gmx-users mailing list gmx-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
--
========================================
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
========================================
--
gmx-users mailing list gmx-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
--
========================================
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
========================================
--
gmx-users mailing list gmx-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
