I will have a look coming Monday. Thanks for reporting that.
Alan
On 24 February 2012 23:25, Kyle Greenway 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
> ma
Kyle, can you send and pdb file so I can reproduce your issue?
Thanks,
Alan
On 24 February 2012 23:25, Kyle Greenway wrote:
>
> Hello,
>
> This email is directed mainly to Alan, who created Acpype.
>
> I've noticed that Acpype has assigned dihedral constants as 0.65084
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 wrote:
> I c
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 wrote:
>
> hi guys,
>
> i'm trying to simulate some receptor ligand s
f your top file?
Alan
On 4 May 2012 14:14, Vedat Durmaz 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 s
; C-CA-
N- H
25 32 31 33 4 180.00 43.93200 2 ; CA- OC1-
C- OC2
I mean, if the parameters that are hiding in e.g.
...gromacs/top/amber99sb.ff could be showed in the top/itp file for human
readers, that would be great.
Thanks,
Alan
--
Alan
ber99sb.ff/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 wrote:
>
>
> On 5/21/12 2:43 PM, Alan wrote:
>
>> Hi there,
>>
>> Is there an op
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 wrote:
>
>
> On 5/22/12 12:46 PM, Alan wrote:
>
>> Hi Justin, your suggestion got close. However, let
am about to implement this workaround for ACPYPE, but just 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@groma
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
On
Or why not trying acpype?
Cheers,
Alan
On 9 September 2011 07:37, Mark Abraham 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 d
convertions, you can do this:
acpype -x disac.inpcrd -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 wrote:
> Hi
that 0.05% (for total pot
energy?) is OK.
Alan
On 15 September 2011 06:18, Yun Shi 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
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 Sept
Indeed, if you do the other way:
0.65084/4.184 = 0.1 ~ 0.156
Alan
On 6 October 2011 08:17, Yun Shi 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,
hen you have to work 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 wrote:
> Hi GROMACS users,
>
> I have used acpype.py t
An update:
Now for NRG-CING, please see:
http://nmr.cmbi.ru.nl/NRG-CING
Best,
Alan
On 3 April 2009 11:31, Alan 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 you
tion.
BTW, acpype -h can show you many more interesting options.
Alan
On 7 June 2013 15:55, Mark Abraham wrote:
> On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
> wrote:
>
> > Hello GMX users,
> >
> > I have some troubles with overriding parameters. I have generated
&g
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. wrote:
> Sorry for the misunderstanding. I should had explained it bette
covalently bonded to another
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 2
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 wrote:
> Hi Grom
Hi, try ACPYPE.
Alan
On 9 October 2013 14:07, xiao 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
And ACPYPE does (besides several others improvements)
Alan
On 9 October 2013 15:24, xiao 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
>
Have you tested your ligand alone in MD simulation and how vmd would show
it?
Alan
On 21 October 2013 08:31, MUSYOKA THOMMAS wrote:
> Dear Users,
> I am doing protein-ligand MD simulations. I first prepare the ligand by
> adding Hydrogen atoms and setting the charges using UCSF c
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 wrote:
> Hi,
> i was trying to generate topology for p-phenylene vinylene polymer fo
Can someone confirm that GMX 4.x is already released with updated
OPLS/AA files as once mentioned in
http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,7/Itemid,26/
?
Many thanks in advance.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of
pu running with x2top.
Mac intel with GMX via Fink.
Many thanks 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.
ting OPLS/AA as
well. I was just trying to find other topol gen tools to compare.
I proper announcement will come soon.
Thanks,
Alan
On Fri, May 8, 2009 at 14:53, wrote:
> From: David van der Spoel
> Justin A. Lemkul wrote:
>>
>> Is this version 4.0.4? I get the same thin
Please, take a look at acpypi.googlecode.com. I hope it can help you.
Alan
On Wed, May 13, 2009 at 06:12, wrote:
> Subject: [gmx-users] DNA-ligand interactions with AMBER
>
> Dear Gromacs users
>
> I am simulating the interactions between ligands and DNA
> using GROMACS wi
Hi There,
Where can I find a summary of the modifications and news about gmx 4.0.5?
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/
still experimental but if you take
information from MKTOP (which I intend to add to ACPYPI eventually) then you
can get something good enough, specially if you do your homework and read
the papers related to this matter.
Cheers,
Alan
Subject: [gmx-users] oplsaa parametrization
>
> Dear Users
Hey Tanos,
You must read some papers but my recommendations are:
GMX 4.0.5 and AMBER99SB forcefield. Look at
http://acpypi.googlecode.comwhere you can find info about how to add
amber forcefield to GMX.
Cheers,
Alan
Subject: [gmx-users] Dynamics with DNA
>
> Hi folks !
> Doe
ms). Otherwise it
would a pleasure to see this issue closely (can you send me your input
prmtop and inpcrd?).
Otherwise do it yourself by making c_ and o_ and the overriding warn will be
off.
Cheers,
Alan
>
> Message: 7
> Date: Thu, 4 Jun 2009 20:55:52 +
> From: Rebeca
an swear it was working before...
Many thanks 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<<
__
Thank you Justin,
You noticed well that. But this example was built to work without
-ignh and to exemplify my problem, because in real case I have this
protein and either I can use 'sed' to fix it (mainly H names) I found
it annoying sometimes, so why not -ignh?
Cheers,
Alan
On M
suite and although I got some fails for complex and
kernel, nothing for simple or pdb2gmx.? Anyway, I doubt tested suite
would fail because oplsaa is working fine here if I do 'pdb2gmx -f
GGG.pdb -ff oplsaa -ignh'
In any case, many thanks for your attention Justin,
Alan
On Mon, Jun 15, 2
Hi Justin,
Just to let you know that after reinstalling everything again with
Fink it worked fine. I have no idea I hade such a problem.
Alan
On Mon, Jun 15, 2009 at 23:05, Alan wrote:
> Hi Justin,
>
> Please, confirm this, you mean that this pdb worked for you with '-ignh'?
programmes one would suggest, why?
Many thanks 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.
e more than
one binary (for different archs) in 'single' file. And yes, a wrapping
script could address that but it's not what I have in mind anyway.
Cheers,
Alan
On Wed, Jun 17, 2009 at 15:16, wrote:
>> Jussi Lehtola skrev:
>> > On Wed, 2009-06-17 at 13:45 +0200, Berk H
mple or gromacs-double.
I hope you can understand me.
Many thanks 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<<
_
to solve a problem with openmpi
in my Fink here.
Cheers,
Alan
On Thu, Jun 18, 2009 at 16:43, wrote:
>
> Alan wrote:
>> Hi List,
>>
>> I would like to know if there's an option in gromacs Makefile that
>> would allow me to once did:
>>
>> ./configure --di
Hi there,
How about taking a look at acpypi.googlecode.com and its wikis?
I hope it can help you.
Alan
On Fri, Jun 26, 2009 at 14:27, wrote:
>
> Hello,
>
> I'm trying to figure out how I can merge the ligand and receptor
> files. I used this script to prep a ligand
, and you can find how to use 'acpypi' for
converting amber topology files to gromacs topol files.
Cheers,
Alan
On Wed, Jul 1, 2009 at 10:25, wrote:
>
> Hi, gmx-users, I have a problem to "translate" nitrogen base residue names
> from AMBER to GROMACS.
> I ha
s and gromacs 4.0.5
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 ma
Dear Mark,
Thanks. I reread those file carefully and noticed the "only implicit
solvent". Sorry for that. I am building my test case here to see by
myself how fast it can be.
Alan
On Sat, Jul 18, 2009 at 11:00, wrote:
> Alan wrote:
>> Hi list, does anyone have an exam
= 2
pbc = no
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78.3
comm_mode = ANGULAR
Many thanks in advance,
Alan
On Sat, Jul 18, 2009 at 11:35, Alan wrote:
> Dear Mark,
>
> Thanks. I reread those file carefully and noticed the "only implicit
> solvent&qu
o em.tpr
mdrun -v -deffnm em
grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr
mdrun -v -deffnm md
vmd md.gro md.trr # OK
mdrun-openmm -v -deffnm md
# 3 times fater
# works fine without set for implicit solvent in md.mdp
# with implicit solvent, md.gro full of nan nan nan everywhere.
vertheless, for those with nvidia cuda and Mac or Windows, it's worth
trying.
Cheers,
Alan
On Sat, Jul 18, 2009 at 18:31, Alan wrote:
> Thanks Justin.
>
> I could swear I tried what you said... anyway it worked now (2.5 x
> faster), but not with implicit solvent for mdrun-op
As I found out by test&error myself, mdrun-openmm will not work with systems
with more than one chain.
Cheers,
Alan
On Tue, Jul 28, 2009 at 15:04, Alan wrote:
> Dear all,
> Zephyr (https://simtk.org/home/zephyr) is released, although only for Mac
> and Windows so far, and
Dear Mark,
I've contacted the authors already. I decided to publish here as well just
to close this topic.
Alan
On Wed, Jul 29, 2009 at 13:45, Alan wrote:
> As I found out by test&error myself, mdrun-openmm will not work with
> systems with more than one chain.
>
> Chee
o use RED to get the charges and then use acpypi to get
the topologies.
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.
>&
nd even though when I was using 10.5.8 (Leopard, 32 bits)
my $PATH was as big as it is and I didn't have problem then.
Many thanks in advance,
Alan
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-u
Thanks Berk, although I didn't test it yet, it makes sense.
Many thanks.
Alan
On Mon, Sep 21, 2009 at 14:10, wrote:
> Hi,
>
> I guess the problem is in src/gmxlib/futil.c,
> where several string buffers that contain the path are of size 512.
> In Gromacs 4.1 they will be
Hi there,
Please, let me suggest to look at acpypi.googlecode.com. You may find
at wikis some answers to your questions.
I hope it helps.
Alan
On Thu, Oct 1, 2009 at 02:34, wrote:
> Message: 2
> Date: Thu, 01 Oct 2009 09:17:02 +1000
> From: Mark Abraham
> Subject: Re: [gmx-user
Also, have a read at acpype.googlecode.com.
Alan
On 21 September 2010 06:36, manoj singh 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 to
carefully.
Then you can come with more specific questions.
Alan
On 21 September 2010 08:03, vivek sharma 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 accepted in gro
Please, let me suggest you acpypi.googlecode.com. There you'll find in
the wikis help about installing gromacs 4.0.5 with support for
ffamber.
Cheers,
Alan
On Tue, Oct 20, 2009 at 12:55, wrote:
> Hi
> I want to use AMBER force fields in gromacs program for md simulation of
> pr-d
As long as not GMX 3.x, the wikis are still valid, no matter which GMX
4.0.x you use.
Alan
PS: thinking twice, the wikis should even work with GMX 3.x as long as
one uses the respective ffamber port.
On Tue, Oct 20, 2009 at 14:38, wrote:
>
> dear Alan
> your suggestion is true.
Dear Carla,
Let me suggest you the wikis at acpypi.googlecode.com.
And then let me ask why amber94 and not amber99sb? And why not trying
acpypi in the link above as I guess it can do pretty much what you
want with much less pain?
Cheers,
Alan
On Tue, Oct 20, 2009 at 15:55, wrote:
>
&
tools straightaway, but
believe me, although antechamber and acpypi can save you a lot of time
and effort, this will only pay off if you do your homework properly.
Thanks to Mark and Justin for addressing his questions.
Cheers,
Alan
On Sun, Oct 25, 2009 at 20:30, wrote:
> Gunnar Widtfe
kbone parameters. Proteins- Structure Function and
Bioinformatics 65, 3 (NOV 15 2006), 712–725.
However, I understand you want to do nucleic acids simulation rather than
proteins, so milage here is low and for that I suggested also the amber
mailing list.
I hope it may helps.
Alan
On Sat, Nov 21, 2009
ould ask you to give more details and even a detailed step by step
of commands of what you're doing including tleap.
Regards,
Alan
On Tue, Dec 1, 2009 at 11:00, wrote:
>
> Thanks for your suggestion, I tried without success and I also tried
> shake. But this is also rather fighti
ged to Fmax < 1000 in 22 steps
#Potential Energy = -6.22813514022256e+04
#Maximum force = 7.58238100790309e+02 on atom 98
#Norm of force = 1.04358667410458e+02
grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
mdrun_d -v -deffnm md
# end commands
Regards,
Alan
On Tue
ore in a long simulation.
Good luck.
Regards,
Alan
On Wed, Dec 2, 2009 at 11:10, Alan wrote:
> Dear Servaas,
>
> In tleap did you really did:
>
> TLEAP
> tleap -f leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> saveamberparm da da_amber.top da_amber.crd
>
>
> If
other things, this capability as you requested.
Cheers,
Alan
On Thu, Jan 28, 2010 at 17:13, Jack Shultz wrote:
> 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 not
>
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, wrote:
>
>
obably not).
Cheers,
Alan
On Fri, Jan 29, 2010 at 11:00, 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 ht
d DNA 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, Hi
ynamic Properties of Amino Acid Analogues: A
> Systematic Comparison of Biomolecular Force Fields and Water Models
>
> J. Phys. Chem. B 110, 17616 (2006)
> http://dx.doi.org/10.1021/jp0641029
>
> Berk
>
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.
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, wrote:
> I am trying to port the new parmbsc0 forcefield (
> http://mmb.pcb.ub.
mple" to port, 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, wrote:
> > Dear Users,
> >
> > I am trying to port the new parmbsc0 forcefield
> > (http://mmb.pcb.ub.es/PARM
Try acpypi:
acpypi.googlecode.com
Alan
> Date: Sat, 18 Oct 2008 00:23:07 -0200
> From: "Ragnarok sdf" <[EMAIL PROTECTED]>
> Subject: [gmx-users] ffamber99 topologies for ligand
> To: gmx-users@gromacs.org
> Message-ID:
><[EMAIL PROTECTED]>
> Co
ok anymore with gmx commands or there's a bug here?
Many thanks 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.
>>
official release. I also suggest to use latest revision o acpypi since I
updated that last week.
I also want people to know that I tested acpypi and ffAMBER for GMX 3.3.1
with GROMACS 4.0.2 and seemed to work like a charm.
Cheers,
Alan
>
> Ragnarok sdf wrote:
> > I am trying to setup a s
ust one more thing, would you mind where are you from and what's your
institute?
Many thanks in advance,
Alan
On Thu, Dec 4, 2008 at 04:01, <[EMAIL PROTECTED]> wrote:
>
> I am working with a system using ffamber99 forcefield and trying to
> set up a ligand protein complex sy
Dear Sorin, what would the differences for ffAMBER 4 from ffAMBER 3?
Many thanks for these release.
Best regards,
Alan
> Date: Tue, 17 Feb 2009 00:04:38 -0800
> From: "Eric J. Sorin"
> Subject: [gmx-users] New ffAMBER Ports
> To:
> Message-ID: <62006d1d26da4
not in spce.itp, why
not? Was it forgotten? Anyone would kindly know something about it?
Cheers,
Alan
>
> Jack Shultz wrote:
> > Hi all,
> >
> > I think I'm having a problem with the water models. Clearly ther are
> > differences in these tip3p models. I can re
NRG-CING here: http://nmr.cmbi.ru.nl/NRG-CING
Please take a look if you find a PDB entry of your interest there!
Cheers,
Jurgen Doreleijers, Alan W.S. da Silva, and Geerten Vuister
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge
I was reviewing *.itp from GMX 4.0.4 and found that we now have _FF_CHARMM
in, e.g., tip3p.itp and spc.itp, but not in spce.itp, why not? Was it
forgotten? Anyone would kindly know something about it?
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of
have problems I guess.
Alan
On Thu, Apr 2, 2009 at 13:48, wrote:
>
> Hi,
>
> CHARMM will be included and fully supported in Gromacs 4.1.
> AMBER on the other hand is provided as an external package.
> This is mainly because is requires some residue renaming and other stuff
&
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 complex is from NMR and deposit in PDB so you can
find it here (http://nmr.cmbi.ru.nl/NRG-CING/index/index.html) already
evaluated.
Cheers,
Ala
Hi there,
I was wondering if Gromacs would have a command to parse a top or itp
file and return a friendly human readable file describing all the
forcefield parameters in a way (for those who knows Amber) that
'rdparm' does for a Amber prmtop file.
Many thanks in advance,
Alan
--
A
ntechamber 1.27? I don't have amber and I am not talking about the
perl version ambconv.pl.
Could it be uploaded at GMX contribution session? The ambconv there is from
2002 and definitely doesn't work anymore.
Many thanks in advance,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Researc
your
topolbuild approach is a very good inspiration since I want to do
something similar from antechamber to generate CNS files with both
topologies PROSLQ and OPLS.
Many thanks,
Alan
> --- Alan <[EMAIL PROTECTED]> wrote:
>
> > Hi list!
> > I gave a good look at GMX mail
On gmx_manual-3.3.pdf, page 101, where one reads:
However if you wat to specify N ...
Should be, I guess:
However if you want to specify N y
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road
"constraints = none"?
I just don't remember where I saw something like this. Any comment here
would be very appreciate.
Many thanks in advance,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court
ely know if GMX is computing the right charge values?
Many thanks in advance.
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
Thanks Peyman and Justin,
So, bottom line, if doing any sort of minimisation (even cg), 'constraints =
none' is fine, right?
Alan
On Wed, Jul 2, 2008 at 7:44 PM, Alan <[EMAIL PROTECTED]> wrote:
> Dears,
> It's more than years that I don't use GMX on regular basi
; temp; echo "Cl 4" >> temp; \mv temp
Protein.top
grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr # total
charge: 8.00e+00
mdrun -v -deffnm em
Many thanks for your attention.
Cheers,
Alan
---
Can you show us your modified ions.itp file (just
sed s/7274/7270/ Protein.top > temp; echo "Cl 4" >> temp; \mv temp Protein.top
grompp -f em.mdp -c Protein_b4em.pdb -p Protein.top -o em.tpr # total
charge: 8.00e+00
mdrun -v -deffnm em
Many thanks for your attention.
Cheers,
Alan
---
Can you show us your
that features I would appreciate very
much your help.
Many thanks 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/
http://www.somewhereville.com/?p=114 it's also wrong there.
Basically, the error is that column cgnr is exchanged with column charge.
"Caveat Emptor"
Cheers,
Alan
On Thu, Jul 3, 2008 at 7:44 AM, Alan <[EMAIL PROTECTED]> wrote:
> Hi List,
> To people using ffamber.
>
Hi List,
Just out of curiosity.
Is there a way of putting integrator steep and md altogether in a
unique mdp file?
Before people start to tell me "you shouldn't do it", let you know
it's just for training purposes, never for production.
Many thanks in advance.
Cheers,
Ala
uot;topol_FAD.itp"
>>>>> #include "topol_ZTRP.itp"
Always put your ligand itp right after #include "ffamber03.itp" (or
whatever forcefield), i.e, never after chains topologies.
This always worked for me. But you have a p
case) are definitely not
called before than in the ligand itp file. So here's where I found the
manual not clear.
Cheers,
Alan
> Message: 4
> Date: Wed, 16 Jul 2008 19:57:33 +0100
> From: Hans Martin Senn <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] About "Invalid or
Hi Erik,
Despite ffamber seems more developed for GMX, can you tell us if
pdb2gmx (for next release) is also working for amber or we still need
to tweak the pdb input file (Nxxx and Cxxx terms, CYN etc.)?
Many thanks in advance,
Alan
> Date: Thu, 17 Jul 2008 21:49:56 +0200
> From: "E
Hi Erik,
Despite ffamber seems more developed for GMX, can you tell us if
pdb2gmx (for next release) is also working for amber or we still need
to tweak the pdb input file (Nxxx and Cxxx terms, CYN etc.)?
Many thanks in advance,
Alan
> Date: Thu, 17 Jul 2008 21:49:56 +0200
> From: "E
Hi list!
I would like to know among mac intel users with Fink, which gromacs
with mpi to use:
gromacs-mpi-lammpi or
gromacs-mpi-openmpi
Or there's any easier way (multi-threads is still not working in GMX, right?)?
Many thanks in advance.
Alan
--
Alan Wilter S. da Silva, D.Sc. -
Thanks vdSpoel,
Just one more question.
So, in a dual/quad core computer, do -sort -shuffle do any difference
for better? I mean, is there use for 'sort and shuffle' in a
multi-core computer (not cluster!)?
Cheers,
Alan
On Tue, Jul 22, 2008 at 4:26 PM, Alan <[EMAIL PROTECTED]>
ith a protein in OPLS/AA force field.
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<<
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