On 2/04/2010 3:07 PM, Lum Nforbi wrote:
Justin,
I appreciate your reply. Actually, I have read through the section
of building parameter files in chap. 5 several times. The only reason
for using atom types instead of numbers is because that is the way they
are represented in the ffcharmmbon.itp and ffcharmmnb.itp files. Numbers
are not used in these force fields. The [ bondtypes ] below is a portion
of the [bondtypes ] listed in the ffcharmmbon.itp file. I will
definitely use numbers.
[ bondtypes ]
; i j func b0 kb
CST OST 1 0.116 784884.928
SS FE 1 0.232 209200.0
C C 1 0.1335 502080.0
CA CA 1 0.1375 255224.0
CE1 CE1 1 0.134 368192.0
CE1 CE2 1 0.1342 418400.0
CE1 CT2 1 0.1502 305432.0
I haven't followed this closely, but perhaps one or other of you has
missed a point here. Even if not, perhaps this description will help
others understand the way the .itp files work.
The [ (bond|angle|etc) ] sections require atom indices (i.e. indices
into the [ atoms ] section) in which pdb2gmx has constructed a three-way
mapping between atom index, atom type and atom name (with help from the
.rtp database). grompp can then use this mapping from atom indices to
atom types to find in the [ (bond|angle|etc)types ] sections the actual
parameter data. Accordingly, the latter sections require atom types. The
[ molecules section ] defines a list of [ moleculetypes ] so that grompp
can also check that the atom ordering is sane, which requires the
aforementioned mapping from atom indices to atom names.
Different force fields use different techniques for things like
1,4-interaction-parameter generation, dihedral lookup and
nonbonded-parameter generation, so making general assertions is tricky.
Mark
Thank you,
Lum
Lum Nforbi wrote:
> Hello all,
>
> I have built a parameter file for the AOT surfactant molecule and
> tried to minimize the energy of a mixture of several of this molecule
> and water molecules but I have the warnings at the bottom part of
this
> mail. Gromacs basically goes through all the lines of parameters
> starting from [ bonds ] and says the parameters are too few. I am
also
> using the charmm force field.
>
> Here is the way I constructed the aot.itp parameter file. I
am not
> sure this is correct. Excerpts of the parameter file are belowl.
>
> - I drew the AOT molecule and did the bond and angle connections
in the
> molecule.The atom names are provided by the ffcharmm27.atp file. All
The .atp file contains atom types, not atom names. Your [bonds],
[angles], etc.
should be numbers, not atom types or names. For instance, if
atoms 1 and 2
are bonded:
[ bonds ]
1 2 (function type, etc)
> values are obtained from the ffcharmmbon.itp file and
ffcharmmnb.itp file.
> - I am not sure how to build the dihedrals since the are X's in the [
> dihedrals ] section of the ffcharmmbon.itp file.
>
As Mark indicated earlier, an X is simply a wildcard - it can
correspond to any
number of atom types.
> My question is: Why does the program say I have few parameters
while I
> just out together parameters from the charmm27 force field?
Please, if I
> am doing something wrong, can someone let me know?
> [ bonds ]
> ; i j func b0 kb
> SL O2L 1 0.1448 451872.0
You're using either atom types or names in these sections, which is
completely
incorrect. Please have a thorough read through Chapter 5 of the manual.
<snip>
> NOTE 1 [file aotwater.top, line 19]:
> System has non-zero total charge: -1.350000e+01
>
I would also be *very* concerned about this line. You have a
negative charge of
-13.5, indicating that whatever charges you've assigned to your
small molecule
have left a fractional charge on the system, which is clearly
non-physical.
-Justin
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file
/usr/local/gromacs/share/gromacs/top/aminoacids.dat
> There are: 60 OTHER residues
> There are: 0 PROTEIN residues
> There are: 0 DNA residues
> Analysing Other...
> Making dummy/rest group for T-Coupling containing 1110 elements
> Making dummy/rest group for Acceleration containing 1110 elements
> Making dummy/rest group for Freeze containing 1110 elements
> Making dummy/rest group for Energy Mon. containing 1110 elements
> Making dummy/rest group for VCM containing 1110 elements
> Number of degrees of freedom in T-Coupling group rest is 3192.00
> Making dummy/rest group for User1 containing 1110 elements
> Making dummy/rest group for User2 containing 1110 elements
> Making dummy/rest group for XTC containing 1110 elements
> Making dummy/rest group for Or. Res. Fit containing 1110 elements
> Making dummy/rest group for QMMM containing 1110 elements
> T-Coupling has 1 element(s): rest
> Energy Mon. has 1 element(s): rest
> Acceleration has 1 element(s): rest
> Freeze has 1 element(s): rest
> User1 has 1 element(s): rest
> User2 has 1 element(s): rest
> VCM has 1 element(s): rest
> XTC has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
>
> NOTE 2 [file aotwater_min.mdp, line unknown]:
> You are using a plain Coulomb cut-off, which might produce
artifacts.
> You might want to consider using PME electrostatics.
>
>
> This run will generate roughly 1 Mb of data
> writing run input file...
>
> There were 2 notes
>
> There were 142 warnings
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.5
> Source code file: gmx_fatal.c, line: 481
>
> Fatal error:
> Too many warnings (142), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> -------------------------------------------------------
>
>
> I appreciate your answers.
>
> Lum
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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