On 5/04/2011 4:59 PM, Geethu Issac wrote:
hello friends,
I am doing simulation of ganglioside gm2 and am getting the following
error.
Fatal error:
Syntax error - File gm2gang.top, line 6
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
Can anyone please help me in this.I
Dear Mark
Actually I don't know why.
I just did the normal process as other my simulations.
Let me discribe my work in details:
I had a protein and a drug,I separated all residues around my drug (2 nm in
radius) by PYMOL
Then I saved the result as protein-new.pdb
So.I used pdb2gmx to generate .to
On 5/04/2011 5:09 PM, mohsen ramezanpour wrote:
Dear Mark
Actually I don't know why.
I just did the normal process as other my simulations.
Let me discribe my work in details:
I had a protein and a drug,I separated all residues around my drug (2
nm in radius) by PYMOL
You can't do that and h
Dear Mark
Thank you for your important notes,I didn't know them.
Then,Can it be resulted from your sentences , there is not any way for
doing simulation with only some parts of a protein?
What can I do if I need simulating only ACTIVE SITE of a protein?Do I have
to simulate the whole of protein
On 5/04/2011 5:39 PM, mohsen ramezanpour wrote:
Dear Mark
Thank you for your important notes,I didn't know them.
Then,Can it be resulted from your sentences , there is not any way
for doing simulation with only some parts of a protein?
What can I do if I need simulating only ACTIVE SITE of a
Dear Mark,
Now, are the files correct?
*EDO.itp*:
[ moleculetype ]
; Name nrexcl
EDO 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1OA 1 EDO OAB 1 -0.111 15.9994
2 H 1 EDO HAE 10.031 1.0080
3
Hello GROMACS USERS,
Does any one have a document/manual/link that describes the name-number atom
type mappings employed in opls-aa?
I would like to build some molecules and specify their parameters, but I see
different of numbers for the same atom type name, e.g:
TYPE NAME
135 CT
136 CT
137
Austin B. Yongye wrote:
Hello GROMACS USERS,
Does any one have a document/manual/link that describes the name-number atom
type mappings employed in opls-aa?
The correspondence between the atom types and bonded types is all contained in
ffnonbonded.itp.
-Justin
I would like to build som
Thanks Justin.
Could you/someone please forward the file? I don't have it.
Austin-
--- On Tue, 4/5/11, Justin A. Lemkul wrote:
> From: Justin A. Lemkul
> Subject: Re: [gmx-users] OPLS-AA atom types
> To: "Discussion list for GROMACS users"
> Date: Tuesday, April 5, 2011, 5:19 AM
>
>
> Austin
Austin B. Yongye wrote:
Thanks Justin.
Could you/someone please forward the file? I don't have it.
It's part of your Gromacs installation. $GMXLIB/oplsaa.ff/ffnonbonded.itp.
If you don't have it, then Gromacs wasn't properly installed and you won't be
able to use whatever force field for w
On 5/04/2011 9:59 PM, ahmet yıldırım wrote:
Dear Mark,
Now, are the files correct?
They're well-formed, but you've not taken Tsjerk's advice and arranged
for (COH)3(NH3+)C to have charges consistent with its symmetry. When
people donate their time to you, please use it or demonstrate why you
On 5/04/2011 11:03 PM, Austin B. Yongye wrote:
Thanks Justin.
Could you/someone please forward the file? I don't have it.
Austin-
Announcing your GROMACS version is an excellent idea. See
http://www.gromacs.org/Support for good suggestions when asking for free
help.
Because you haven't, we
Dear experts,
Hi,
When prepare a system, the system had +5.5. So I add 5 CL- ion to neutralize.
But as you know, the Cl charge is -1 and there still is 5e-2. how can i remove
that.
i want to make totally neutral system.
Thank you.
Hyun--
gmx-users mailing listgmx-users@gromacs.org
http:
Hyunsik wrote:
Dear experts,
Hi,
When prepare a system, the system had +5.5. So I add 5 CL- ion to neutralize.
But as you know, the Cl charge is -1 and there still is 5e-2. how can i remove
that.
i want to make totally neutral system.
Fractional charges like these indicate that your t
On 5/04/2011 11:17 PM, Hyunsik wrote:
Dear experts,
Hi,
When prepare a system, the system had +5.5. So I add 5 CL- ion to neutralize.
But as you know, the Cl charge is -1 and there still is 5e-2. how can i remove
that.
Your statements are inconsistent. If you had 5.5 charge and added five
Hi all,
I'm trying to compile release 4.5.4 on a system that has been running
every release since 4.0.4 without a problem. Even 4.5.3 compiled fine
with the following configure:
LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib"
CPPFLAGS="-I/cvos/shared/apps/fftw/gcc/64/3.2/include" ./configu
Pablo Englebienne wrote:
Hi all,
I'm trying to compile release 4.5.4 on a system that has been running
every release since 4.0.4 without a problem. Even 4.5.3 compiled fine
with the following configure:
LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib"
CPPFLAGS="-I/cvos/shared/apps/fftw/g
Justin:
I am using gromacs version 4.0.2. Several attempts to download current gromacs
versions from http://www.gromacs.org/Downloads kept yielding 93.0-byte files.
So I re-installed my pre-existing v4.0.2 without any problems (>./configure
--enable-sse; make; make install).
If you could send me
Austin B. Yongye wrote:
Justin:
I am using gromacs version 4.0.2. Several attempts to download current gromacs
versions from http://www.gromacs.org/Downloads kept yielding 93.0-byte files. So I
re-installed my pre-existing v4.0.2 without any problems (>./configure
--enable-sse; make; make in
Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances of CT with
diferent opls_??? numbers, but no indication of their environments; they could
represent C bonded to 1->4 carbon atoms, etc. There's no way of telling. I
contacted one of the opls folks last week, but
On 6/04/2011 1:00 AM, Austin B. Yongye wrote:
Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances of CT with
diferent opls_??? numbers, but no indication of their environments; they could
represent C bonded to 1->4 carbon atoms, etc. There's no way of telling. I
On 6/04/2011 1:28 AM, Mark Abraham wrote:
On 6/04/2011 1:00 AM, Austin B. Yongye wrote:
Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances
of CT with diferent opls_??? numbers, but no indication of their
environments; they could represent C bonded to 1->4 carbo
Mark Abraham wrote:
On 6/04/2011 1:28 AM, Mark Abraham wrote:
On 6/04/2011 1:00 AM, Austin B. Yongye wrote:
Thanks Justin.
It still doesn't solve my problem, e.g., there are several instances
of CT with diferent opls_??? numbers, but no indication of their
environments; they could represent
Dear gmx-users,
Im trying to modify the ffbonded.itp file of Gromos43a1 ff in Gromacs
4.5.3 version, in order to add parameters for my modified Cys residue.
However, I have some difficulties in understanding what are the
parameters already included in this file. In particular, ffbonded.itp
file ap
anna.marabo...@isa.cnr.it wrote:
Dear gmx-users,
I’m trying to modify the ffbonded.itp file of Gromos43a1 ff in Gromacs
4.5.3 version, in order to add parameters for my modified Cys residue.
However, I have some difficulties in understanding what are the
parameters already included in this file
dear gromacs users,
I'm solvating my protein in nitrogen box. I have changed my
spc216.gro, spc.itp and spce.itp files. I face the following error.
How can I fix it?
invalid line in /usr/share/gromacs/top/spc216.gro for atom 407:
0.41200 0.41200 0.41200
thanks in advance.
Best regards,
sarah k wrote:
dear gromacs users,
I'm solvating my protein in nitrogen box. I have changed my
spc216.gro, spc.itp and spce.itp files. I face the following error.
Changed? In what way? If you're solvating with nitrogen, why are you dealing
with water coordinates and topologies?
How can
Em 02-04-2011 0:33, Justin A. Lemkul escreveu:
Marcelo Silva wrote:
Hi,
I am trying to simulate mixtures of ethanol and trifluoroethanol and
I would like to use the same parameters used on OPLS parametrization.
On the OPLS1996 paper the authors starts by stating that they've used
267 mole
Marcelo Silva wrote:
Em 02-04-2011 0:33, Justin A. Lemkul escreveu:
Marcelo Silva wrote:
Hi,
I am trying to simulate mixtures of ethanol and trifluoroethanol and
I would like to use the same parameters used on OPLS parametrization.
On the OPLS1996 paper the authors starts by stating tha
On 6/04/2011 4:30 AM, sarah k wrote:
dear gromacs users,
I'm solvating my protein in nitrogen box. I have changed my
spc216.gro, spc.itp and spce.itp files.
Don't. In the last 48 hours, I posted a procedure that used genconf to
make a box of solvent of a given density.
I face the followi
I don't know if it is possible or not. I think that you can enhance
your chances of developer attention if you develop a small and simple
test system that reproduces the slowdown and very explicitly state
your case for why you can't use some other method. I would suggest
posting that to the
In this case,
Can't you just use pdb2gmx to regenerate the topology file from the merged
gro which will resolve the separate moleculechains for you?
On 2011-03-30 04:25:34AM -0500, Mark Abraham wrote:
> On 30/03/2011 8:14 PM, Ghassen Hassani wrote:
>
> Dear Friends,
> Right now i am worki
Peter C. Lai wrote:
In this case,
Can't you just use pdb2gmx to regenerate the topology file from the merged
gro which will resolve the separate moleculechains for you?
Only if you really feel like re-writing the ligand topology from scratch as an
.rtp entry to be processed by pdb2g
> Date: Tue, 5 Apr 2011 23:43:19 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
>
> On 5/04/2011 11:17 PM, Hyunsik wrote:
> > Dear experts,
> >
> > Hi,
> >
> > When prepare a system, the system had +5.5. So I add 5 CL
김현식 wrote:
> Date: Tue, 5 Apr 2011 23:43:19 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
>
> On 5/04/2011 11:17 PM, Hyunsik wrote:
> > Dear experts,
> >
> > Hi,
> >
> > When prepare a system, the system
Are TPR files compatible across minor gromacs version changes?
Like if I have a TPR generated under 4.5.3 can I feed it into mdrun on 4.5.4
or should I re-grompp my initial files?
Thanks
--
===
Peter C. Lai | University o
Peter C. Lai wrote:
Are TPR files compatible across minor gromacs version changes?
Like if I have a TPR generated under 4.5.3 can I feed it into mdrun on 4.5.4
or should I re-grompp my initial files?
Minor versions shouldn't present a problem. According to src/gmxlib/tpxio.c,
the .tpr vers
Hi to all,
I want to know what do Coul-SR,LJ-SR,Coul-14 and LJ-14 mean in g_energy ? I
do know SR stands for short range.But do short range really mean? Thanks!
Coul-SR:K-SOL 46 LJ-SR:K-SOL 47 Coul-14:K-SOL 48 LJ-14:K-SOL
Zh
zhongjin wrote:
Hi to all,
I want to know what do Coul-SR,LJ-SR,Coul-14 and LJ-14 mean in g_energy
? I do know SR stands for short range.But do short range really mean?
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy
-Justin
Thanks!
Coul-SR:K-SOL 46 LJ-SR:K-SOL 47 Coul-14
Hello
I am constructing a ligand for which I wish to use the new Charmm CGenFF
parameters (a long aliphatic ketone).
I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:
For reference, c36 lipid CTL3 atoms (in the case of POPC) map to CG331
in CGenFF; they are
Dear Dr.Justin
I had the same problem.
I modified the charges and charge groupsin the topology of a drug.the net
charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:
NOTE:The system has non-zero total charge: 3.03e00
I continued simulation and ign
Dear Dr.Justin
What can we do (how can neutralize system) if the total charge of our system
was not integer?
I think there is not any solution and we have to simulate a charged system
not a neutral.
Am I right?
Thanks in advance
On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour <
ramezanpour.m
On 6/04/2011 2:51 PM, Peter C. Lai wrote:
Hello
I am constructing a ligand for which I wish to use the new Charmm CGenFF
parameters (a long aliphatic ketone).
I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:
For reference, c36 lipid CTL3 atoms (in the case
On 6/04/2011 4:42 PM, mohsen ramezanpour wrote:
Dear Dr.Justin
I had the same problem.
I modified the charges and charge groupsin the topology of a drug.the
net charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:
NOTE:The system has non-zero tota
On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:
Dear Dr.Justin
What can we do (how can neutralize system) if the total charge of our
system was not integer?
I think there is not any solution and we have to simulate a charged
system not a neutral.
Am I right?
I suspect every tutorial for si
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