Hi
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions
On 9/12/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for
Hi,
These are the parameters I kept in the .rtp file for DMPC molecule. Still
getting same error message should I need to look at somewhere else.
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate
On 9/12/13 1:17 PM, Rama Krishna Koppisetti wrote:
1. Did you re-run pdb2gmx after modifying the .rtp file?
Yes.. I do run with modified .rtp file but output was same as previous.
2. Have you looked into the [bonds] directive in the .top file that pdb2gmx
created to see if anything is out of
1. Did you re-run pdb2gmx after modifying the .rtp file?
Yes.. I do run with modified .rtp file but output was same as previous.
2. Have you looked into the [bonds] directive in the .top file that pdb2gmx
created to see if anything is out of place? Every line should have 5
entries:
[bonds]
On 9/12/13 2:57 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
Output topology from pdb2gmx. You could see some entries differ between
two molecules.
I'm looking forward to do restrained MD for this system by using Gromacs.
[ moleculetype ]
; Namenrexcl
Protein 3
[
Hi Justin,
Output topology from pdb2gmx. You could see some entries differ between
two molecules.
I'm looking forward to do restrained MD for this system by using Gromacs.
[ moleculetype ]
; Namenrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr
On 9/12/13 11:03 AM, Rama Krishna Koppisetti wrote:
Hi,
These are the parameters I kept in the .rtp file for DMPC molecule. Still
getting same error message should I need to look at somewhere else.
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
Hi Justin,
Should I use R-B dihedrals for DMPC lipids rather than periodic
dihedrals.
I'm getting an Error message like,
ERROR 18815 [file topol.top, line 54180]:
No default Ryckaert-Bell. types
ERROR 18816 [file topol.top, line 54181]:
No default Ryckaert-Bell. types
--Rama
On
On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
Should I use R-B dihedrals for DMPC lipids rather than periodic
dihedrals.
You should use whatever the force field tells you.
I'm getting an Error message like,
ERROR 18815 [file topol.top, line 54180]:
No default
Hi Justin,
These type of dihedrals I'm using now, Is it correct format.
[ dihedral
s
]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
LH1 LOS LC2 LC22 35.26 334.72
LC LOS LO LP22 0.00 167.36
LC LOS LO LP22 0.00
On 9/11/13 9:57 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
These type of dihedrals I'm using now, Is it correct format.
[ dihedral
s
]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
LH1 LOS LC2 LC22 35.26 334.72
LC LOS LO LP22
Those lines are related to DMPC lipid dihedrals.
-_Rama
On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
Should I use R-B dihedrals for DMPC lipids rather than periodic
dihedrals.
You should use
On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote:
Those lines are related to DMPC lipid dihedrals.
I know that much. I am trying to extract some actual detail here so I can help
you reach a conclusion. The error indicates line numbers in the topology. On
those line numbers are a
Sorry.., Justin
Yes.. It is a sequence of atom numbers from DMPC atoms. The errors are
coming from all DMPC atoms dihedrals only not by protein dihedrals.
--Rama
On Wed, Sep 11, 2013 at 9:08 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote:
Hi,
I wrote an entry in the rtp file of the force field OPLS-AA + Berger lipid
parameters
[ DMPC ]
[ atoms ]
;ai Ber_type charge resnr mass
CN1LC30.4000115.0350
CN2LC30.40001 15.0350
CN3LC30.4000115.0350
NTMLNL
On 9/11/13 6:19 PM, Rama Krishna Koppisetti wrote:
Hi,
I wrote an entry in the rtp file of the force field OPLS-AA + Berger lipid
parameters
[ DMPC ]
[ atoms ]
;ai Ber_type charge resnr mass
CN1LC30.4000115.0350
CN2LC30.40001 15.0350
Hi Justin,
This is another type of error while running energy minimization:
what to do for these type of errors.
ERROR 218 [file topol.top, line 23487]:
No default Ryckaert-Bell. types
ERROR 219 [file topol.top, line 23499]:
No default Ryckaert-Bell. types
ERROR 220 [file topol.top, line
On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
This is another type of error while running energy minimization:
what to do for these type of errors.
They're exactly the same as the dihedral error from before. You're using
parameters that don't exist in the force field.
Hi Justin,
It is which part in the force field. Exactly which file I have to look to
overcome this errors.
Thanks
--Rama
On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
This is another type of error
On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote:
Hi Justin,
It is which part in the force field. Exactly which file I have to look to
overcome this errors.
Go to the line number in the .top indicated in the error message and determine
the atom types. This will tell you the sequence of
Adding parameters can be a little bit of a pain, you could instead change
the atom types in the molecule parameter, to ones that have defined angles
and bond types with each other. Of course, you would need to make sure that
you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc.
On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote:
Adding parameters can be a little bit of a pain, you could instead change
the atom types in the molecule parameter, to ones that have defined angles
and bond types with each other. Of course, you would need to make sure that
you dont
On 9/10/13 3:55 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is
there any suggestions from you.
You've constructed the force field such that you have repeating entries that
override parameters. You still haven't said
How so? If there is an atom type that has a reasonable similarity to the
one that doesnt have the default bondtypes, what makes using that worse
than coming up with entirely new parameters that are not necessarily based
on physical data or quantum calculations? Isnt copying angles and force
Hi Justin,
There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is
there any suggestions from you.
WARNING 1 [file ffbonded.itp, line 2817]:
Overriding Proper Dih. parameters.
Use dihedraltype 4 to allow several multiplicity terms.
old: 180 5.86 1 180 5.86 1
new: LNL
On 9/10/13 3:54 PM, Rafael I. Silverman y de la Vega wrote:
How so? If there is an atom type that has a reasonable similarity to the
one that doesnt have the default bondtypes, what makes using that worse
than coming up with entirely new parameters that are not necessarily based
on physical
On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
The force field that I constructed with OPLS + Berger lipids
.
Similar to
your Bilayer tutorial.
Presumably you are following Chris Neale's half-epsilon, double pairlist method
then? In any case, you're defining the same
Hi,
How to convert normal dihedrals to so-called Ryckaert-Bellemans
potential dihedrals. Is there any script available for that.
Thanks
Rama
On Tue, Sep 10, 2013 at 3:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
The force
On 9/10/13 6:10 PM, Rama Krishna Koppisetti wrote:
Hi,
How to convert normal dihedrals to so-called Ryckaert-Bellemans
potential dihedrals. Is there any script available for that.
Periodic dihedrals and R-B dihedrals have different functional forms. See the
manual.
-Justin
--
H
i Justin,
The force field that I constructed with OPLS + Berger lipids
.
Similar to
your Bilayer tutorial.
Thanks
--Rama
On Tue, Sep 10, 2013 at 3:26 PM, Rama Krishna Koppisetti
ramkishn...@gmail.com wrote:
--
gmx-users mailing listgmx-users@gromacs.org
Ok..I got it
Thanks Justin...
--Rama
On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti
ramkishn...@gmail.com wrote:
Hi Justin ,
I prepared .rtp files for lipid. what is the exact command to merge two
chains in gromacs.
On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul
Hi Justin ,
I prepared .rtp files for lipid. what is the exact command to merge two
chains in gromacs.
On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
Thanks for your reply.
How to do that?
If
Hi Justin,
I included 1 DMPC molecule parameters in the file should I need to include
128 molecules parameters in the file .rtp.
Thanks
--Rama
On Mon, Sep 9, 2013 at 4:43 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I merge two
Hi Justin,
I merge two molecules as a single molecule type. Now I'm trying to do
energy minimization of the system, getting errors like
Fatal error: [file topol.top, line 55130]:
No default Proper Dih. types
Any idea for this type of errors.
Thanks
--Rama
On Mon, Sep 9, 2013 at 1:57
On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I included 1 DMPC molecule parameters in the file should I need to include
128 molecules parameters in the file .rtp.
No. Residue definitions are used any time they are encountered in the
coordinate file. There is no need for
On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I merge two molecules as a single molecule type. Now I'm trying to do
energy minimization of the system, getting errors like
Fatal error: [file topol.top, line 55130]:
No default Proper Dih. types
Any idea for this type of
... and probably the use of grompp -maxwarn 5 is hiding problems that
you should be fixing first!
Mark
On Sun, Sep 8, 2013 at 1:03 AM, Justin Lemkul jalem...@vt.edu wrote:
On 9/7/13 6:55 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
If you are willing to see my complex pdb file or complex
Hi Justin,
I use similar procedure as you mentioned in the tutorial to generate my
topologies for protein and bilayer. there is no .rtp file for lipid. Is
there any reference to include lipid molecule in aminoacid.rtp file.
Thanks
Rama
On Fri, Sep 6, 2013 at 4:57 PM, Justin Lemkul
On 9/7/13 6:40 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I use similar procedure as you mentioned in the tutorial to generate my
topologies for protein and bilayer. there is no .rtp file for lipid. Is
there any reference to include lipid molecule in aminoacid.rtp file.
Read the manual
Hi Justin,
If you are willing to see my complex pdb file or complex .gro file and
topology files, I'll send you for the reference.
Thanks
Rama
On Sat, Sep 7, 2013 at 5:42 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/7/13 6:40 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
I use
On 9/7/13 6:55 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
If you are willing to see my complex pdb file or complex .gro file and
topology files, I'll send you for the reference.
At present, I do not have the time to spare trying to work this out myself. The
manual has all the detail
Sorry ..,here are my distance restraints file:
[ distance_restraints ]
;ai ajtypeindextype'low
up1up2fac
3012679 1 0 1 0.0
1.62142.2111.0
3012696
On 9/6/13 5:23 PM, Rama wrote:
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy
NMR experimental data.
Without restraints there is no problem, but if I include distance restraints
in topology file, getting fatal error:
the lipid atom index # was not
On 9/6/13 5:27 PM, Rama Krishna Koppisetti wrote:
Sorry ..,here are my distance restraints file:
Without context as to what these numbers are, there's little useful information
here. I suspect you're trying to implement restraints between protein and lipid
atoms, which will not work for
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy
NMR experimental data.
Without restraints there is no problem, but if I include distance restraints
in topology file, getting fatal error:
the lipid atom index # was not recognized by using this command:
g_grompp
H
i Justin,
Thanks for your reply.
How to do that?
On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/6/13 5:23 PM, Rama wrote:
Hi,
I'm doing NMR restrained MD simulation for protein-Bilayer system to
satisfy
NMR experimental data.
Without restraints there
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
Thanks for your reply.
How to do that?
If .rtp entries exist for your lipid with the force field, it's simply a matter
of pdb2gmx -merge, choosing which chains should be written as a single
[moleculetype]. If the lipids are
On 9/6/13 5:56 PM, Rama Krishna Koppisetti wrote:
Hi Justin ,
Is there any script available in gromacs documentation or some where?
My guess is no. Ask Google.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of
Hi Justin ,
Is there any script available in gromacs documentation or some where?
Thanks
On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote:
H
i Justin,
Thanks for your reply.
How to do that?
If .rtp entries
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