On 6/10/13 9:11 AM, Steven Neumann wrote:
Thank you Justing. Last question - each of my amino acid is one bead. How
can I specify [angles ] between atoms corresponding to different residues?
Shall I add it at the end of my rtp entry with all amino acids?
Each .rtp entry should only contain one bead, right? The only way to define
angles for such a system is to use +/- prefixes for succeeding and preceding
residues (beads).
-Justin
On Mon, Jun 10, 2013 at 2:05 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/10/13 9:04 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/10/13 8:53 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 6/10/13 8:42 AM, Justin Lemkul wrote:
On 6/10/13 8:40 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 6/10/13 8:23 AM, Steven Neumann wrote:
Dear Gmx Users,
I created my own CG force field and i process my structure to
pdb2gmx.
I
process 3 beads I created to check whether the topology is properly
created:
Using the CG force field in directory ./CG.ff
No file 'watermodels.dat' found, will not include a water model
Reading 60central_Carbons.pdb...
Read 3 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id
changing.
There are 1 chains and 0 blocks of water and 3 residues with 3
atoms
chain #res #atoms
1 'X' 3 3
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./CG.ff/atomtypes.atp
Atomtype 1
Reading residue database... (CG)
Opening force field file ./CG.ff/aminoacids.rtp
Reading .rtp file without '[ bondedtypes ]' directive,
Will proceed as if the entry
[ bondedtypes ]
; bonds angles dihedrals impropers all_dihedrals nr_exclusions
HH14
remove_dih
1 1 1 2 0
3
1
1
Residue 13t at the beginning of ./CG.ff/aminoacids.rtp
Sorting it all out...
Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 'X' (3 atoms, 3 residues)
Identified residue MET1 as a starting terminus.
Identified residue VAL3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Now there are 3 residues with 3 atoms
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...There are 0 dihedrals, 0 impropers,
0
angles
0 pairs, 0 bonds and 0 virtual sites
Total mass 319.420 a.m.u.
Total charge 1.000 e
Writing topology
Back Off! I just backed up posre.itp to ./#posre.itp.2#
Writing coordinate file...
Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2#
--------- PLEASE NOTE ------------
You have successfully generated a topology from:3Carbons.pdb.
The CG force field is used.
--------- ETON ESAELP ------------
gcq#304: "Gabba Gabba Hey!" (The Ramones)
It stated that there are no angles.
However in my ffbonded.itp which i ncluded in my forcefield.itp
[ angletypes ]
; i j k funct th0 C0 C1 C2 C3 C4
CME CSE CVA 6 0 0.0680894 -0.0328291000 590330
-46.3 13
How Gromacs can read this angle?
[angletypes] simply define possible interactions, but are not
used
unless
there are [angles] in the .rtp that use them. pdb2gmx writes angles
based
on bonds, but if you note above, there are zero bonds, so pdb2gmx
cannot
write any angles. Does your .rtp entry specify [angles] but no
[bonds]?
I want to use constraints with SHAKE as bonds...no harmonic bonds. In
this
case pdb2gmx will never create angles? Shall I also manually add [
angles ]
to my top then?
Yes, because in the absence of bonds, even [angles] in .rtp entries
are
ignored.
Thinking a bit more though, it's probably a lot easier to define
bonds
and
let pdb2gmx do the work for you. Using:
constraints = all-bonds
constraint-algorithm = shake
will turn all bonds in the topology into constraints, which sounds like
exactly what you want to do.
-Justin
Thank you. But specifying [ bonds ] in my rtp file without force
constant?
Entries need to be syntactically correct, but the force constant is
completely irrelevant if you are constraining all bonds.
Shall i remove [ bonds ] from my top file then?
What? Without [bonds], you can't do what I'm suggesting. If you don't
have [bonds], you have to write [constraints] and [angles] (and any other
bonded directories) manually.
I am saying about removing them from top after pdb2gmx just to bring [
angles ] to top - I do not want to have a harmonic or any potential for
bonds.
I suppose you can do that, but why bother? If you want to constrain all
bonds with SHAKE, see above. There will be no harmonic potential anywhere
if all bonds are constrained.
-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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