Hi, this feature is really really experimental and should indeed be
avoided. If opls you want, then give a try with
http://www.aribeiro.net.br/mktop/
Alan
On 8 November 2013 04:42, aditya sarma adityasrm...@gmail.com wrote:
Hi,
i was trying to generate topology for p-phenylene vinylene
Have you tested your ligand alone in MD simulation and how vmd would show
it?
Alan
On 21 October 2013 08:31, MUSYOKA THOMMAS mutemibiochemis...@gmail.comwrote:
Dear Users,
I am doing protein-ligand MD simulations. I first prepare the ligand by
adding Hydrogen atoms and setting the charges
Hi, try ACPYPE.
Alan
On 9 October 2013 14:07, xiao helitr...@126.com wrote:
Dear all,
I am doing membrane protein simulation by using amber force field. The
lipid force field parameters are from the lipid11.dat from Amber. Firstly,
i got the xx.prmtop and xx.prmcrd files, and then i used
And ACPYPE does (besides several others improvements)
Alan
On 9 October 2013 15:24, xiao helitr...@126.com wrote:
Hi Alan,
Thank you very much! The problem is solved. The reason is that amb2gmx
cannot distinguish the proper and improper dihedrals.
Best wishes
Fugui
At 2013-10-09
In https://code.google.com/p/acpype/ you can look the wikis and you see the
explanations about the partial charges.
The best solution, though not straightforward, would be using
http://q4md-forcefieldtools.org/REDS/
Alan
On 2 September 2013 11:27, Muhammad Ayaz Anwar ayazan
molecule. If one wants parameters for a modified amino acid residue, one
way of getting it is by neutralising the N- and C- termini of the 2
adjacent residues (so make a tripeptide) and then fit manually the
additional parameters to the modified residue.
Alan
On 17 July 2013 14:30, Melchor S. msm
Hi there,
You said ACPYPE didn't work… Can you give details? Have you try with GAFF
first? If you don't mind, can you post me your molecule in private email?
Thanks,
Alan
On 9 July 2013 22:34, Melchor S. msm...@cid.csic.es wrote:
Sorry for the misunderstanding. I should had explained
-h can show you many more interesting options.
Alan
On 7 June 2013 15:55, Mark Abraham mark.j.abra...@gmail.com wrote:
On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
bat.demou...@gmail.comwrote:
Hello GMX users,
I have some troubles with overriding parameters. I have generated
checking first
if someone has a better idea/suggestion.
Alan
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Hi, the issue is not with Antechamber or Acpype. There were similar
questions to yours here (try searching GMX mail archives). The problem is
you need to create the GBSA.itp parameters for you ligand.
Which Acpype does is to create/convert Amber/GAFF parameters to usual MD in
Gromacs.
Alan
Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.
Cheers,
Alan
On 22 May 2012 12:36, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/22/12 12:46 PM, Alan wrote:
Hi Justin, your suggestion got close. However, let me give
/forcefield.itp any combination that handles parameters for
X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral?
Thanks,
Alan
On 21 May 2012 18:50, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/21/12 2:43 PM, Alan wrote:
Hi there,
Is there an option in pdb2gmx that when generating
Hi there,
look at 'acpype -h', in particular:
-g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top
file
Alan
On 3 May 2012 14:34, Vedat Durmaz dur...@zib.de wrote:
hi guys,
i'm trying to simulate some receptor ligand system with implicit
?
Alan
On 4 May 2012 14:14, Vedat Durmaz dur...@zib.de wrote:
thanks justin and alan.
i also had the suspicion that the error is caused by case sensitivity.
simply replacing all atom types from lower to upper case within the
ligand.itp file yields the same error: missing gb parameters
Hi Thales,
Amber 1.5? You mean Amber12 and ambertools12?
I haven't test with them yet, but it would help me if you run in the debug
mode and post the output here for me:
acpype -di proteinname.mol2 -c user
Thanks,
Alan
On 26 April 2012 19:02, Thales Kronenberger kronenberg...@gmail.com
Kyle, can you send and pdb file so I can reproduce your issue?
Thanks,
Alan
On 24 February 2012 23:25, Kyle Greenway kgree...@sfu.ca wrote:
Hello,
This email is directed mainly to Alan, who created Acpype.
I've noticed that Acpype has assigned dihedral constants as 0.65084 for
many
hard in literature to find parameters and likely make
use of RED for getting a more quantum mechanics approach for your
parameters and charges.
Good luck,
Alan
On 23 November 2011 10:35, madhumita das madhumita.bioi...@gmail.comwrote:
Hi GROMACS users,
I have used acpype.py to convert
An update:
Now for NRG-CING, please see:
http://nmr.cmbi.ru.nl/NRG-CING
Best,
Alan
On 3 April 2009 11:31, Alan alanwil...@gmail.com wrote:
We've recently announced iCing, which includes whatif as well. Please,
take a look at http://nmr.cmbi.ru.nl/cing/Home.html.
If it happens that your
Hello gmx-users
I have been attempting to obtain van der Waal's volumes using the g_sas
utility. The command I use to do so is something like
g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg
This seems to give reasonable results for most of my test systems, however when
I run the
Indeed, if you do the other way:
0.65084/4.184 = 0.1 ~ 0.156
Alan
On 6 October 2011 08:17, Yun Shi yunsh...@gmail.com wrote:
Hi Alan,
So is acpype using a conversion factor of 4.184 for dihedral force
constant?
I found some dihedral constants as 0.156 in the amber format, which
Hi Yun,
ACPYPE is working fine. What happens here is I choose the reproduce the
exact values one sees in AMBER.
Now why GMX tip3p file choose a different value, I don't know.
Nevertheless, it's pretty simple to put whatever value you want there if you
think you need.
Alan
On 26 September 2011
that 0.05% (for total pot
energy?) is OK.
Alan
On 15 September 2011 06:18, Yun Shi yunsh...@gmail.com wrote:
Hi Alan,
For example, in the Glycam_06g.dat file, you can find:
OH-CG-CG-OS 1 -1.10 0.0-1
So this dihedral parameter has a force
-p disac.prmtop --gmx45
If you have sander, you can do just one step of EM and compare against one
step EM with GMX. Do the proper conversions and Energies diff should be
0.001%.
Cheers,
Alan
On 12 September 2011 21:21, Yun Shi yunsh...@gmail.com wrote:
Hi all,
I am not a CS person, but I
Or why not trying acpype?
Cheers,
Alan
On 9 September 2011 07:37, Mark Abraham mark.abra...@anu.edu.au wrote:
On 9/09/2011 4:21 PM, Yun Shi wrote:
Hi all,
I understand this problem has been discussed before, but it seems no
conclusion has been drawn.
Someone needs to do some work
Dear gmx_users,
I have a question regarding the 4.5.4 version of gromacs, and the g_energy
program.
In the past I had used g_energy with the -aver option, which would give me
partial
sums along with my instantaneous energy values at each output step. This
allowed
me to take the difference
Hi Liao,
Your python installation seems to be missing the datetime module, which is
very bizarre. Please verify your Python installation, you may have issues
with your PYTHONPATH.
Regards,
Alan
2011/4/12 fancy2012 fancy2...@yeah.net
Hi GMX users,
When I ran acpype.py on my computer, I got
]
C[2] -= 4 * V[period]
C[4] += 4 * V[period]
So, as you can see, I can handle up to 4 periods (C[5] is always 0, but not
with ILDN and I need to add C[6] rules as well).
Any ideas? Many thanks in advance,
Alan
--
Alan Wilter SOUSA da SILVA, DSc
and above.
But I don't want to fuss about it. If to forget about GMX 4.0.x and below is
the way, so it will be.
Thanks,
Alan
On 31 March 2011 16:08, David van der Spoel sp...@xray.bmc.uu.se wrote:
On 2011-03-31 15.27, Alan Wilter Sousa da Silva wrote:
Hi there,
Since ILDN dihedrals has some
A 3.39967e-01 3.59824e-01
And using GMX 4.5 and I don't see this complain anymore:
WARNING 1 [file system_GMX.top, line 43]:
Overriding atomtype CA
Should I assume that gromacs finally made its atomtypes case sensitive? Only
version 4.5 and above?
Many thanks,
Alan
On 21 August 2008 09
Have a good look in acpype, specially its wiki. There you'll see that acpype
is totally new code and among other things it covers amb2gmx.pl and solves
several of its drawbacks. It's not perfect though but for a system created
in tleap, the project is likely to be completed converted to gmx.
Alan
Have a look at acpype.googlecode.com
Alan
2010/12/23 gromacs564 gromacs...@126.com
Hi ,
I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam
web(they are glycam06 force field,included in AMBER) , but cannot converted
this amber files to gromacs files format
Also, have a read at acpype.googlecode.com.
Alan
On 21 September 2010 06:36, manoj singh mks.am...@gmail.com wrote:
First, you have to develop parameter for your molecule withing Amber. Then
you have to create .prmtop and .inpcrd files for your molecule, and than you
can convert the Amber
carefully.
Then you can come with more specific questions.
Alan
On 21 September 2010 08:03, vivek sharma viveksharma.i...@gmail.com wrote:
Hi,
Thanks Manoj and Alan for your quick response. I am already using the
ambertools to generate the topology and these topologies are
successfully
to Andersen thermostat only at
section 6.9 GROMACS on GPUs. Is it supposed to be used only with mdrun-gpu?
Any ideas? Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http
fine except GMX.
Bizzarely but gmx 4.5 beta were compiling ok.
I will try release-4-5-patches updated later.
Thanks,
Alan
On 13 September 2010 12:58, Rossen Apostolov ros...@kth.se wrote:
Just to add: the pre-built OpenMM-2.0 for Mac are compiled for 32bit. If
you get an error as:
Linking
make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all]
Error 2
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court
a propose.
And there programmes that observe this column, like openbabel. If converting
this pdb to mol2 I got wrong structure since babel thinks I am dealing with
Helium atoms.
In gmx 4.0.x the last column was never printed so never had this problem
before.
Thanks,
Alan
--
Alan Wilter S. da
Hi there,
Now that gromacs 4.5.1 is released I was wondering which branch should I
checkout if I want to test the bleeding edge gromacs development.
Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court
,
Alan
On 7 September 2010 11:57, Carsten Kutzner ckut...@gwdg.de wrote:
Hi Alan,
'bleeding edge' gromacs development is as always in the 'master' branch.
The latest bugfixes for the 4.5.x versions you are going to find in the
'release-4-5-patches' branch.
Carsten
On Sep 7, 2010, at 12
gmx bin
in /usr/local/bin. I praise consistency.
Thanks,
Alan
On 7 September 2010 13:05, Rossen Apostolov rossen.aposto...@cbr.su.sewrote:
On 9/7/10 1:19 PM, Alan wrote:
I am trying release-4-5-patches and now I can see it's compiling and
installing. However, 'make install' puts the bins
/CMakeFiles/gmx_gpu_utils.dir/all]
Error 2
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2
Same thing with gmx from git. Any idea? Thanks.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis
Just one more question. How are you handling CYS? In amber it could be CYP,
CYN etc.
Thanks a lot,
Alan
On 25 August 2010 13:59, Berk Hess g...@hotmail.com wrote:
Hi,
I now turned on the automatic HIE, and analogous, terminal renaming on by
default.
Berk
handling CYS? In amber it could be CYP,
CYN etc.
Thanks a lot,
Alan
On 25 August 2010 13:59, Berk Hess g...@hotmail.com wrote:
Hi,
I now turned on the automatic HIE, and analogous, terminal renaming on by
default.
Berk
--
From: g...@hotmail.com
To: gmx
in some problems, 99% my
fault of course.
Thanks a lot for your prompt replies.
Best,
Alan
On 25 August 2010 16:06, Berk Hess g...@hotmail.com wrote:
Hi,
This is completely unrelated.
Eric changed all the names to allow processing of his ports by Gromacs
version 3.3 and 4.0.
In 4.5 I
/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:
In function ‘nb_kernel400nf_x86_64_sse’:
/Users/alan/Programmes/gromacs/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629:
error
and if there's conflict,
ignore all changes in my side and revert any modification to what's in the
repository.
Is it possible with git?
Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2
, Alan wrote:
Hi there,
I want to change from release-4-5-patches to master
I am trying:
git reset master
git checkout master
git pull
error: Your local changes to 'include/resall.h' would be overwritten by
merge. Aborting.
Please, commit your changes or stash them before you can merge
Ok, doing:
git reset origin/release-4-5-patches
git checkout origin/release-4-5-patches
git pull
Already up-to-date.
restored the sanity of system.
On 24 August 2010 13:52, Alan alanwil...@gmail.com wrote:
Thanks Carsten, but now nothing is not working, not even what was doing so:
git reset
Thanks Berk, it seems to be working now.
Alan
On 24 August 2010 08:54, Berk Hess g...@hotmail.com wrote:
Hi,
This was due to two simultaneous issues. I fixed them both for the next
beta release.
Note that using HIS iso HISE as a residue name would solve the problem.
For 4.5 this should
-t origin/master
fatal: git checkout: branch master already exists
git branch
master
* release-4-5-patches
# didn't change, let's try another command (and here starts my 'guessing'
experiment)
git checkout master
Switched to branch 'master'
# nice it works!
Thanks,
Alan
On 24 August 2010 14:14
and proceed.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo
residue HIE3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
---
Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d748b
Source code file: /Users/alan/workspace/gromacs/src/kernel/pdb2top.c, line:
916
Fatal error
NE214 NE231
HIS2 NE231 0.854
HIS3 NE248 0.751 0.847
---
Program pdb2gmx, VERSION 4.5-beta3-dev-20100824-d6298
Source code file: /Users/alan/workspace/gromacs/src/kernel/resall.c, line:
552
Fatal error:
Residue 'HISE' not found
/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line:
583
Fatal error:
Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh
to figure out a way?
I've read http://tools.ietf.org/html/rfc1832.html and for reference, see
topic 6. AN EXAMPLE OF AN XDR DATA DESCRIPTION.
My other option would be using a parsing code to read g_energy output but
this seems very silly.
Many thanks in advance,
Alan
--
Alan Wilter S. da Silva, D.Sc
pot energy for amber force fields.
I don't know about charmm here, but I thought amber dihe parameters were
sort multiple terms and as far as I remember, the need to convert proper
dihe to RBs was necessary for early versions of gromacs 3.x, am I right?
Best,
Alan
On 18 August 2010 22:01, Alan
when multiple parameter lines are present the same atom types for a
dihedral type 9.
Berk
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users
: 5.605193857299268e-45
# Ok, what that means?
Any help here would be appreciated.
Many thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx
.
Many thanks you all.
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx-users@gromacs.org
http
of Sorin, amber impr. dih are treated as prop. dih in
gromacs.
Many thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing list
Thanks, it's working now.
Alan
On 11 August 2010 17:59, Alan alanwil...@gmail.com wrote:
Hi there,
I cannot download from
http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMMany
file and link to Gamess-UK seems to be broken as well.
Alan
--
Alan Wilter S. da
Thanks,
I saw your commits at gromacs git and cmake worked fine now.
Alan
On 11 August 2010 17:34, Alan alanwil...@gmail.com wrote:
Hi there,
I am using gromacs from git source with cmake on Mac SL with Fink.
~/Programmes/gromacs% git show
commit 86226a1a075a071920b0413aa7030545f8e6e282
- fftpack
-- Loaded CMakeASM-ATTInformation - ASM-ATT support is still experimental,
please report issues
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/alan/Programmes/gromacs/build
dhcp-128-232-144-215[2416]:~/Programmes/gromacs/build% make mdrun
[ 0%] Building
+0200
Fixed a reverted version string in configure.ac
BTW, is there simpler way to say the revision number in git like 'svn
info'?
Thanks
Alan
On 12 August 2010 12:11, Alan alanwil...@gmail.com wrote:
Hi there,
I am trying now to compile mdrun-openmm, by doing:
cmake -DGMX_OPENMM
in advance,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo
%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_membed.c.o
Linking C static library libgmxana.a
[ 85%] Built target gmxana
make: *** [all] Error 2
Any help would be appreciated, many thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University
Hi there,
I cannot download from
http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMMany
file and link to Gamess-UK seems to be broken as well.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis
specific reason, I find this quite annoying.
GMX 4.5 still doesn't address this.
So, is there plans to bring rtp atom nomenclature to the latest PDB
standards or this task is not necessary (and I missing something else)
or only in gmx 5 when pdb2gmx gets smarter?
Many thanks in advance,
Alan
Thanks Roland, it did work.
Cheers,
Alan
On Sun, Aug 1, 2010 at 09:46, gmx-users-requ...@gromacs.org wrote:
Alan,
with the following change your example works for me.
diff --git a/src/gmxlib/inputrec.c b/src/gmxlib/inputrec.c
index 581ae4c..e148612 100644
--- a/src/gmxlib/inputrec.c
For gmx 4.5 beta, I see with ./configure --help:
--without-qmmm-mopacUse modified Mopac 7 for QM-MM (see website)
--without-qmmm-mopacUse ORCA for QM-MM
What that really means?
Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry
Hi there,
I am trying gmx 4.5 beta on Mac SL 10.6.4 with Fink, doing:
./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib --enable-shared
--with-gsl --with-x
and then 'make' failed with:
(cd .libs/libgmx.lax/libthread_mpi.a ar x
/Users/alan/Downloads/gromacs-4.5-beta1/src/gmxlib/thread_mpi
To myself.
Removing --enable-shared and compilation went fine.
Alan
On Sat, Jul 31, 2010 at 11:41, Alan alanwil...@gmail.com wrote:
Hi there,
I am trying gmx 4.5 beta on Mac SL 10.6.4 with Fink, doing:
./configure CPPFLAGS=-I/sw/include LDFLAGS=-L/sw/lib --enable-shared
--with-gsl
) and more warnings.
Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org
for the command above with:
---
Program grompp, VERSION 4.5-beta1
Source code file: inputrec.c, line: 161
Software inconsistency error:
Unknown epc value
Any ideas? Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
with at least 6 decimals instead of the usual 3.
Many thanks,
Alan
On Tue, Jul 27, 2010 at 20:34, gmx-users-requ...@gromacs.org wrote:
Alan: you should try Ilja's suggestion, it was a good one. The idea is
that during pdb2gmx you may have obtained a .gro file that was rounded
and then you
and parameters. Any ideas of
what could be missing here?
Many thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing list
when using pdb2gmx_d to be like:
gro (single or double): 2ALA N 13 0.192700 0.178900 0.165000
Hummm I don't like this.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA
:5.87%
Angle: 3.49%
Dihe:0.14%
vdW: 0.52%
Elec:0.17%
Pot.Tot: 5.90%
I am very surprised to find this difference, in special for Bond since it's
for this term essentially the same equation and parameters. Any ideas of
what could be missing here?
Many thanks,
Alan
--
Alan Wilter
Hi there,
I didn't have time to improve opls generation in ACPYPE. I need to put a
Wiki about it for the moment, but to get the Opls atomtypes, use MKTOP:
http://labmm.iq.ufrj.br/mktop/
Good luck,
Alan
On Tue, Jul 20, 2010 at 14:42, gmx-users-requ...@gromacs.org wrote:
Hello all
I want
of ffamber and acpype? Since you said you
have the parameters for glycerol you may not need to build the topology
anew, but I do recommend looking at acpype.googlecode.com to know more about
simulations involving amber ff and gromacs, besides links to important
resources like ffamber.
Cheers,
Alan
answer is yes and my attempt to to answer that is above.
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx
Thanks Mark, here is the answer I got from Amber list and explains what I
saw.
Cheers,
Alan
This is an issue with the force field and has been noted several times
before. I would take a look at the mailing list archive (
http://archive.ambermd.org) - search
been happy with the results, even comparing with REDS.
Best regards,
Alan
-Justin
The mol2 structure code (with incorrect Gasteiger charges) is written
below (and attached as NAD.mol2 with corresponding PNG structure image).
Thanks in advance,
Nancy
--
Alan Wilter S. da Silva
,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx
, be sure that you have the right protonation state and try to
re-run your case putting CONECT info in the pdb just to check it.
I hope it helps.
Best,
Alan
On Fri, Jun 4, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote:
hi alan and all others,
i love it. i've probably never seen
of execution: 7s
Ah, ok, I should've know this... It's a fall back routine to try to use
'sleap', but sleap is broken in AmberTools 1.3 and 1.4, unfortunately.
Thanks for trying acpype.
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University
for the
confusion!
If you are familiar to ambertools (tleap mainly), so you can create your
molecule there, save the amber parameters and use acpype to convert from
amber to gromacs format.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University
the topology with acpype but months to write the
code, so if you'd take some few minutes to read and use an updated version
(it's not acpypi anymore BTW)...
BTW, how did you get this message cannot find template for residue C3N in
our library?
acpype.googlecode.com
Regards,
Alan
--
Alan Wilter S
(which is mostly designed for Amber FF) and then
MKTOP for getting the oplsaa atom types.
Feel free to contact.
Best regards,
Alan
On Tue, May 18, 2010 at 01:28, gmx-users-requ...@gromacs.org wrote:
Message: 2
Date: Mon, 17 May 2010 12:58:09 -0400
From: Justin A. Lemkul jalem...@vt.edu
Hi Ran!
Good point, in Lippert et al. they didn't use (or is not clear) thermostats.
And yes, I guess you're right.
Thanks
Alan
On Fri, May 14, 2010 at 09:27, gmx-users-requ...@gromacs.org wrote:
Hi Alan,
I don't think using single precision is much of a problem when using
thermostats
precision, e.g.
normal mode analysis).
Essentially I would like to understand better this double x single approach
in MD re accuracy.
Thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA
extra impr. dihedrals are
added, but clearly not necessary.
You may want to try ACPYPE as I believe antechamber does a really good job
getting the topology (even if in excess of imp. dih as for TRP and probably
for napthalene), and of course check the literature as suggested by Justin.
Alan
On Wed
amb2gmx in general, so I would be glad if
you could take a look at it and if you could let me know which modifications
you did to amb2gmx.
I am taking plunge in this problem again and I'll try to come out with a
solution based in what you suggest.
Cheers,
Alan
On Fri, Apr 9, 2010 at 00:53, gmx-users
doing to test.
Thanks again,
Alan
On Fri, Apr 9, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote:
Hi Alan,
I have no experience with acpypi, so I can't tell which one does better,
or why... rdparm not being needed, that would be a strong point.
Unfortunately, I'm running a bit short
I strongly advice you to contact Eric Sorin from ffAMBER project as he's
onto that and you maybe can add to his efforts.
http://ffamber.cnsm.csulb.edu/
Alan
On Wed, Apr 7, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote:
I am trying to port the new parmbsc0 forcefield (
http
, then it would have been
done since the first version of ffamber, but I know Eric Sorin is working on
that now.
Alan
On Wed, Apr 7, 2010 at 22:00, gmx-users-requ...@gromacs.org wrote:
Dear Users,
I am trying to port the new parmbsc0 forcefield
(http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0
without lipids. And
if using membranes, what would be the water model recommended.
Suggestion of references for reading are more than welcome.
Thanks,
Alan
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton
other things, this capability as you requested.
Cheers,
Alan
On Thu, Jan 28, 2010 at 17:13, Jack Shultz j...@drugdiscoveryathome.comwrote:
Hi,
I was trying to figure out if there is a short-cut for what I'm doing. I
have complexes that I'm trying to prep using pdb2gmx. The ligand does
on complex.pdb and have pdb2gmx to *know* about the ligands
and generated the respective top and gro files ready for EM and MD.
It is that what I understood Jack wants and what you said you have added to
the coming pdb2gmx (for gmx 4.1?).
Many thanks,
Alan
On Fri, Jan 29, 2010 at 09:28, gmx-users-requ
,
Alan
On Fri, Jan 29, 2010 at 11:00, gmx-users-requ...@gromacs.org wrote:
of them. So you can just put, e.g., a file called ligand.itp in your
force
field or current dir and pdb2gmx
will read it.
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org
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