On 12/16/12 12:52 AM, James Starlight wrote:
Justin,
It's not quite understood for me why such errors occurs in the atoms
of standard residues when I've bounded them to the C term of my
chromophore if the geometry of the adjacent residues might not be
changed. So it likely that some errors
Justin, thanks again for explanation.
So the first 5 atoms in cmap.it correspond to the starting sequence of
the backbone atoms of the amino acid doesnt it ? So what is the 24 24
numbers at the end of each cmap line ?
E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would
be
On 12/16/12 10:34 AM, James Starlight wrote:
Justin, thanks again for explanation.
So the first 5 atoms in cmap.it correspond to the starting sequence of
the backbone atoms of the amino acid doesnt it ? So what is the 24 24
numbers at the end of each cmap line ?
Probably something related
The last problem with which I've forced during preparation of my
chromophore is when I've defined bond between chromophore and the next
residue
C+N
That produce 15 addition errors about unknown UB and dihedral types
in the atoms of the next residue (not in the chromophore) where all UB
and
On 12/14/12 11:42 PM, James Starlight wrote:
The topology with the below params produced that 118 errors during
grompp processings ( after pdb2gmx processing the geoetry of the
mollecule was correct )
[CRN]
[ atoms ]
CG2 CA-0.0900 0
CD1 CA-0.0800 1
CD2 CA-0.0800 2
CE1 CA
On 12/15/12 1:34 PM, James Starlight wrote:
The last problem with which I've forced during preparation of my
chromophore is when I've defined bond between chromophore and the next
residue
C+N
That produce 15 addition errors about unknown UB and dihedral types
in the atoms of the next
So as I understood it've happened because the conformation of the
adjacent residue is differ when that residue bounded to the
chromophore ( in comparison to the residue in unbound capped form).
But in term of the backbone geometry of C and N-terms chromophore is
like a typical amino acid. Also
On 12/15/12 2:18 PM, James Starlight wrote:
So as I understood it've happened because the conformation of the
adjacent residue is differ when that residue bounded to the
chromophore ( in comparison to the residue in unbound capped form).
Conformation is irrelevant; atom types are all that
Justin,
It's not quite understood for me why such errors occurs in the atoms
of standard residues when I've bounded them to the C term of my
chromophore if the geometry of the adjacent residues might not be
changed. So it likely that some errors occur during parametrization of
the molecule which
Today I've tried to rename atoms from Swiss's params specific names to
the standard charmm names and obtain the set of the same errors
No default Improper Dih. types
No default U-B types
No default Bond types
Its strange to me because chromophore itself consist of only one
uncommon bond (in
On 12/14/12 2:28 PM, James Starlight wrote:
Today I've tried to rename atoms from Swiss's params specific names to
the standard charmm names and obtain the set of the same errors
No default Improper Dih. types
No default U-B types
No default Bond types
Its strange to me because chromophore
Justin,
in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp to the existing charmm parameters(
it's uncommon
On 12/14/12 3:20 PM, James Starlight wrote:
Justin,
in the case of the system with the atom types assigned from that paper
the grompp produced above 118 errors of non standard bond, angle as
well as dihedral types ;o So it' seems that some 118 addition terms
must be added to the ffbonded.itp
The topology with the below params produced that 118 errors during
grompp processings ( after pdb2gmx processing the geoetry of the
mollecule was correct )
[CRN]
[ atoms ]
CG2 CA-0.0900 0
CD1 CA-0.0800 1
CD2 CA-0.0800 2
CE1 CA-0.2800 3
CE2 CA-0.2800 4
CZ CA 0.4500
Also I've made the same parameters with the capped chromophore (NH2 on
the C-term (instead of OH) and ACE on the N term (instead of H).
When I've defined that chromophore as the Protein I've obtained an error
Fatal error:
Atom OXT in residue CRO 66 was not found in rtp entry CRO with 38 atoms
Oh that problem was imperically resolved by renamind O2 ( which are
not terminal but pdb2gmx define them as a terminal ) atom to O3
The only question about my chromophore is the definition of the IMPROPER groups.
As I've posted above my initial model was CAPPED from C and N termi by
NH2 and Ace.
On 12/12/12 12:37 AM, James Starlight wrote:
That the mollecule that I made
[ CRO ]
[ atoms ]
CG2 CB 0.0284 0
CD1 CB -0.1500 1
CD2 CB -0.1500 2
CE1 CB -0.1500 3
CE2 CB -0.1500 4
CZCB 0.0825 5
HLH 0.3600 39
NRNH1-0.9900 6
CA1 CR
On 12/12/12 6:54 AM, James Starlight wrote:
Oh that problem was imperically resolved by renamind O2 ( which are
not terminal but pdb2gmx define them as a terminal ) atom to O3
The only question about my chromophore is the definition of the IMPROPER groups.
As I've posted above my initial
Justin,
The IMPROPERS consisted of atom names (its correct as I understood).
The bond tern I've changed. The resulted RTP
[CRO]
[ atoms ]
CG2 CB 0.0284 0
CD1 CB-0.1500 1
CD2 CB-0.1500 2
CE1 CB-0.1500 3
CE2 CB-0.1500 4
CZ CB 0.0825 5
NNC=O -0.7301 6
CA1 CR
New problem during processing of y structure via GROMPP
ERROR 217 [file topol.top, line 34183]:
No default Improper Dih. types
ERROR 218 [file topol.top, line 34184]:
No default Improper Dih. types
ERROR 219 [file topol.top, line 34185]:
No default Improper Dih. types
ERROR 220 [file
On 12/12/12 11:49 AM, James Starlight wrote:
New problem during processing of y structure via GROMPP
ERROR 217 [file topol.top, line 34183]:
No default Improper Dih. types
ERROR 218 [file topol.top, line 34184]:
No default Improper Dih. types
ERROR 219 [file topol.top, line 34185]:
Justin,
That errors was strange to me because I've already used Swiss's ITP
files for diffusional ligands including them in the topol.top of my
protein and there were no such errors about non-standart types in any
terms. It seems that some additions to the ffbonded.itp also required
besides the
On 12/12/12 3:11 PM, James Starlight wrote:
Justin,
That errors was strange to me because I've already used Swiss's ITP
files for diffusional ligands including them in the topol.top of my
protein and there were no such errors about non-standart types in any
terms. It seems that some additions
Peter, thanks for explanations!
Could you tell me is it possible to convert CGenFF output for
hetatomic group to the RTP (not an itp ) gromac's data ?
I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein
which is consist of HETTATOMIC chromophore covently bonded to the
On 12/11/12 6:04 AM, James Starlight wrote:
Peter, thanks for explanations!
Could you tell me is it possible to convert CGenFF output for
hetatomic group to the RTP (not an itp ) gromac's data ?
I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein
which is consist of
Today I've made parametrization of the chromophore group by means of
Swiss param and integrated that topology into charmm27 ff. The only
problem that I have is with the N-term N atom of the chromophore. It's
likely that I made mistake to parametrize it into full protonated form
(NH2).
When I've
On 12/11/12 4:13 PM, James Starlight wrote:
Today I've made parametrization of the chromophore group by means of
Swiss param and integrated that topology into charmm27 ff. The only
problem that I have is with the N-term N atom of the chromophore. It's
likely that I made mistake to parametrize
That the mollecule that I made
[ CRO ]
[ atoms ]
CG2 CB 0.0284 0
CD1 CB -0.1500 1
CD2 CB -0.1500 2
CE1 CB -0.1500 3
CE2 CB -0.1500 4
CZCB 0.0825 5
HLH 0.3600 39
NRNH1-0.9900 6
CA1 CR 0.3310 7
CB1 CR 0.2800 8
CG1 CR
Today I've performed test simulation of the protein-cAMP complex with
the charmm27 force field and obtain good stable system. I've compared
polar contacts of my complex ( ligand have been done with SwissParam)
with the X-ray structure of that protein solved with the same complex
and obtained
On 2012-12-08 03:20:54AM -0800, James Starlight wrote:
1- on what assumptions that blocks were generated ?
This appears to be a swissparm-specific question. I don't know what
algorithms it uses to match what are essentially pharmacophores in the new
molecule with the common individual blocks it
Today I've tried to simulate complexes of my protein with the cyclic
GMP parametrized by ATB's. (below the recent parametrisation for
charges of that molecule done by am1 algorithm)
[ moleculetype ]
; Name nrexcl
_N4P 3
[ atoms ]
; nr type resnr resid atom cgnr chargemass
On 12/7/12 10:41 AM, James Starlight wrote:
Today I've tried to simulate complexes of my protein with the cyclic
GMP parametrized by ATB's. (below the recent parametrisation for
charges of that molecule done by am1 algorithm)
[ moleculetype ]
; Name nrexcl
_N4P 3
[ atoms ]
; nr type
Justin,
ligand-only simulation in vacuum have been finished with the same errors :)
Step 19200, time 38.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous,
On 12/7/12 11:42 AM, James Starlight wrote:
Justin,
ligand-only simulation in vacuum have been finished with the same errors :)
Step 19200, time 38.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atoms 1 and 3)
bonds that rotated more than
Justin,
following to your advise I've tried to use charmm 27 ff for simulation
of my protein-cGMP complex ( ligand was parametrized by Swiss Param
server).
Could you provide me with the cut-offs for vdw as well as
electrostatics suitable for simulation in charmm27 and 36 force
fields?
Does
On 12/7/12 1:19 PM, James Starlight wrote:
Justin,
following to your advise I've tried to use charmm 27 ff for simulation
of my protein-cGMP complex ( ligand was parametrized by Swiss Param
server).
Could you provide me with the cut-offs for vdw as well as
electrostatics suitable for
Justin,
with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
NOTE 1 [file ./mdps/em.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rvdw.
NOTE 2
On 12/7/12 2:21 PM, James Starlight wrote:
Justin,
with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
NOTE 1 [file ./mdps/em.mdp]:
For energy conservation with switch/shift potentials, rlist should
On 12/6/12 2:39 AM, James Starlight wrote:
Justin,
Could you provide me with the example of the server where I could
obtain Gromac's itp topologies for the charmm ff? I know many such
servers which could be useful only for preparation systems for NAMD
program.
Google CHARMM ligand topology
Justin,
Thanks again for explanation.
It's interesting that above parametrization made by ATB have cased the
system to crash within first ps of modeling ;) (On the contrarythe
system with the ligand made by prodrg have been very stable during
100ns). I ve tried to re-parametrized my molecule by
On 12/5/12 12:57 PM, James Starlight wrote:
Dear Gromacs Users!
In one of my study I investigate interactions of the cyclic
nucleotides (cGMP and cAMP) with some cyclic-nucleotide-binding
proteins. I'm modelling that complexes in the gromos 56a7 ff with the
parameters for ligands made by
Justin,
Indeed the force field is the 54a7 ( modiffied version of the 54a6).
The main reason of using GROMOS ff in that case was the topology of
ligands which could be easily created by means of prodrg or ATB. On
other hand I've never worked with the protein-ligand complexes in
charmm ff for
On 12/5/12 1:39 PM, James Starlight wrote:
Justin,
Indeed the force field is the 54a7 ( modiffied version of the 54a6).
The main reason of using GROMOS ff in that case was the topology of
ligands which could be easily created by means of prodrg or ATB. On
other hand I've never worked with
Justin,
Could you provide me with the example of the server where I could
obtain Gromac's itp topologies for the charmm ff? I know many such
servers which could be useful only for preparation systems for NAMD
program.
By the way recently I've made parametrization of my cGMP molecule by
means of
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