[gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 61
Farial Tavakoli
faryal.tavakoli at gmail.com
Sun Oct 28 07:44:30 CET 2018
Dear Bhupendra
Thank you for your replying.
I typed the same command that you said: conda install -c acpype -c
openbabel -c ambermd
but the system said :
conda: command not found
or but when I typed : "python acpype.py -i XXX.pdb -b XXX -o gmx" or
"python acpype.py -i XXX.mol2 -o gmx" faced to this error:
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2018 AWSdS |
============================================================================
ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting !
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
What 'which antechamber' in your terminal says?
'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second
I would be appreciated it if you can help me
Best regards
Farial
On Wed, Oct 24, 2018 at 10:17 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: acpype (neelam wafa)
> 2. Simulated tempering (Gregory Man Kai Poon)
> 3. Re: parameters for plotting 2D density map with gmx densmap
> and xpm2ps (Wenjuan Jiang)
> 4. Re: Adding residue to .rtp file (Raji)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 24 Oct 2018 20:57:45 +0500
> From: neelam wafa <neelam.wafa at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] acpype
> Message-ID:
> <CA+ZtqOGAF1dujrJsjkGYKH_ng3PTAj-H7V7xPEyxs=
> oU0-yM2A at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi alan
>
> Can you please tell how long will it take for the online acpype server to
> be available?
>
> Regards
> Neelam wafa
>
> On Wed, 24 Oct 2018, 6:23 pm Alan, <alanwilter at gmail.com> wrote:
>
> > Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
> > will have more things to show eventually.
> >
> > Alan
> >
> > On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar <
> > bhupendra.dandekar001 at gmail.com> wrote:
> >
> > > I actually got lot of help from Luciano Kagami about installation and
> > usage
> > > of acpype and ligro.
> > > Thanks to both of you.
> > >
> > > Bhupendra
> > >
> > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
> > > bhupendra.dandekar001 at gmail.com> wrote:
> > >
> > > > Thanks to you also sir.
> > > > Your work is really appreciated and is really helpful.
> > > >
> > > >
> > > > Bhupendra
> > > >
> > > > On Wed, Oct 24, 2018 at 3:59 PM Alan <alanwilter at gmail.com> wrote:
> > > >
> > > >> Thanks Bhupendra, indeed we have this option, which is experimental,
> > but
> > > >> I'm glad to see some are already using it and it seems to be
> working.
> > > >>
> > > >> Alan
> > > >>
> > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> > > >> bhupendra.dandekar001 at gmail.com> wrote:
> > > >>
> > > >> > Dear Farial,
> > > >> >
> > > >> > Use this command to install acpype and antechamber using conda:
> > > >> >
> > > >> > conda install -c acpype -c openbabel -c ambermd
> > > >> >
> > > >> > and then you can check and call acpype, antechamber like this from
> > > your
> > > >> > terminal:
> > > >> >
> > > >> > acpype -h
> > > >> > antechamber -h
> > > >> >
> > > >> > then you can generate ligand topology using this command:
> > > >> >
> > > >> > acpype -i FFF.pdb -b FFF -o gmx
> > > >> >
> > > >> > Hope this helps. Let me know if you have any questions.
> > > >> >
> > > >> > Thanks
> > > >> > Bhupendra
> > > >> >
> > > >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
> > > >> faryal.tavakoli at gmail.com
> > > >> > >
> > > >> > wrote:
> > > >> >
> > > >> > > Dear GMX useres
> > > >> > >
> > > >> > > I am trying to convert .OFF and .FRCMOD files obtained from
> AMBER
> > > >> > parameter
> > > >> > > database (Bryce Group: Computational Biophysics and Drug Design
> -
> > > >> > > University of Manchester)
> > > >> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the
> > format
> > > >> that
> > > >> > > GROMACS is compatible with in .rtp files*. so referred to
> GROMACS
> > > >> > tutorial
> > > >> > > protein-ligand complex and downloaded acpype. installed it using
> > its
> > > >> > > readme.txt file but whenever i typed ../acpype.py -i FFF.pdb
> > At
> > > >> > folder
> > > >> > > *acpype/test* (/Downloads/acpype-master/acpype) or
> > > >> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> > > >> > >
> > > >> > >
> > > >> > > *bash: ../acpype.py: No such file or directory*
> > > >> > >
> > > >> > > *while when I typed whereis acpype in terminal , the operating
> > > system
> > > >> > says
> > > >> > > :*
> > > >> > >
> > > >> > >
> > > >> > > *acpype: /usr/local/bin/acpype*
> > > >> > > * it means there is the executable file of acpype . so how come
> I
> > > type
> > > >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO
> such
> > > >> file or
> > > >> > > directory?*
> > > >> > > *Is there anyone who ca help me?*
> > > >> > > *I really would be appreciated it if one help me to solve this
> and
> > > can
> > > >> > > convert the AMBER format files to GRMACS format files.*
> > > >> > >
> > > >> > > *best regards*
> > > >> > > *Farial*
> > > >> > > --
> > > >> > > Gromacs Users mailing list
> > > >> > >
> > > >> > > * Please search the archive at
> > > >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > before
> > > >> > > posting!
> > > >> > >
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> > > >> > >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > >> > > send a mail to gmx-users-request at gromacs.org.
> > > >> > >
> > > >> > --
> > > >> > Gromacs Users mailing list
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> before
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> > or
> > > >> > send a mail to gmx-users-request at gromacs.org.
> > > >> >
> > > >>
> > > >>
> > > >> --
> > > >> *I**? have just cycled* from Land's End to John O'Groats??? (the
> > > >> whole Britain!)
> > > >> for a charity, would you consider? ?supporting my? cause?
> > > >> http://uk.virginmoneygiving.com/AlanSilva
> > > >> --
> > > >> Alan Wilter SOUSA da SILVA, DSc
> > > >> Senior Bioinformatician, UniProt
> > > >> European Bioinformatics Institute (EMBL-EBI)
> > > >> European Molecular Biology Laboratory
> > > >> Wellcome Trust Genome Campus
> > > >> Hinxton
> > > >> Cambridge CB10 1SD
> > > >> United Kingdom
> > > >> Tel: +44 (0)1223 494588
> > > >> --
> > > >> Gromacs Users mailing list
> > > >>
> > > >> * Please search the archive at
> > > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > >> posting!
> > > >>
> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >>
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> > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > >> send a mail to gmx-users-request at gromacs.org.
> > > >
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
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> > > posting!
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> >
> >
> >
> > --
> > *I**? have just cycled* from Land's End to John O'Groats??? (the
> > whole Britain!)
> > for a charity, would you consider? ?supporting my? cause?
> > http://uk.virginmoneygiving.com/AlanSilva
> > --
> > Alan Wilter SOUSA da SILVA, DSc
> > Senior Bioinformatician, UniProt
> > European Bioinformatics Institute (EMBL-EBI)
> > European Molecular Biology Laboratory
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD
> > United Kingdom
> > Tel: +44 (0)1223 494588
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 24 Oct 2018 16:27:10 +0000
> From: Gregory Man Kai Poon <gpoon at gsu.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] Simulated tempering
> Message-ID: <6c0bb7f5-4d07-13a1-06a5-d688e0a43103 at gsu.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> I am attempting to do simulated tempering on GROMACS 2016.3.? In my
> preliminary googling, I have found several questions from different
> people on the procedure in the past few years but unfortunately without
> response.? I have read up on the literature on the few papers that
> described ST with GROMACS, but have not had much success with the
> authors.? From studying the mdp options, it appears that ST is handled
> under the general umbrella of expanded ensemble simulations.? I am
> therefore hopeful that I could learn from those of you who may not be
> doing ST, but are using related mdp options and are willing to help me out.
>
> Specifically, I am looking for how to extract the updated weights used
> to determine the Metropolis transitions in the MC moves.? I can get
> information such as temperature and lambda in gmx energy, and
> kinetic/potential energy and dH from the output md.xvg.? I've looked in
> md.log.? However, I can't find where the weights are stored.
>
> I would also be thankful for any links on ST with GROMACS that I have
> missed.
>
> Best wishes,
>
> Gregory
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 24 Oct 2018 11:24:43 -0700
> From: Wenjuan Jiang <sibylaries at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] parameters for plotting 2D density map with
> gmx densmap and xpm2ps
> Message-ID:
> <CAJFfpqpfK9wLmM7UCfvqzMWT-2FrjoM6=
> X_3vRV+ntHUdVFdvw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi St?phane
>
> I am interested in the lipid density around the protein, so I only choose
> the lipid bilayer to plot 2D density map.
>
> Regarding the coordinates, I need to remove the pbc box effect by 'pbc mol'
> of trajconv function so that the protein will be complete, or in Amber,
> cpptraj with autoimage function, and this will not affect the function of
> densmap and xpm2ps. The 2D without pbc will look like pieces of protein. In
> this sense, I think yes, you need to do preprocessing before 2D densemap
>
> Best,
> Wenjuan
>
> On Wed, Oct 24, 2018 at 1:21 AM ABEL Stephane <Stephane.ABEL at cea.fr>
> wrote:
>
> > Hi Wenjuan,
> >
> > Thank you for response is it useful. I have an additional question, did
> > you plot in the same xpm figure the 2D dens profiles for the protein and
> > the lipids (since I suppose you simulated in a membrane)?
> >
> > An additional comment, here
> > Since your channel was simulated in a bilayer you used the xtc generated
> > during the MD without coordinate manipulations (correct ?). In my case,
> the
> > MP is inserted in a micelle and thus the MP detergent complex can freely
> > rotate move during the MD so I need to reorient the complex according
> the z
> > axis "before" to use gmx densmap, correct ?
> >
> > Thanks you
> >
> > St?phane
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 23 Oct 2018 23:31:22 -0700
> > From: Wenjuan Jiang <sibylaries at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] parameters for plotting 2D density map with
> > gmx densmap and xpm2ps
> > Message-ID:
> > <CAJFfpqotdvMwTW5zkQPtYBTPETcr7HqY4ZzhL7j=
> > SPrhAA8trA at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hello St?phane,
> >
> > I happened to use densmap and xpm these days for my ion channel.
> >
> > Here is an example that you can play with for your system.
> >
> > gmx densmap -f md.xtc -s md.tpr -n index.ndx -aver z -bin 0.05 -dmin 0
> > -dmax 20 -unit nm-2 -o md.xpm
> > ( later choose the group you are interested in)
> >
> > -aver z means we want to get top view, that is going to show your dense
> map
> > in xy plane.
> > -bin width, you can play with it to get best view. more options, you can
> > check with densmap -h
> >
> > gmx xmp2ps -f md.xpm -o md.eps -rainbow blue
> >
> > eps file can be opened either by eps viewer or photoshop.
> >
> > Thanks,
> > Best
> > Wenjuan
> >
> >
> > On Tue, Oct 23, 2018 at 7:49 AM ABEL Stephane <Stephane.ABEL at cea.fr>
> > wrote:
> >
> > > Dear all,
> > >
> > > I would like to obtain a 2D density map plot as for instance Fig. 4 in
> > the
> > > following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein
> > > inserted in a surfactant micelle with gmx densmap and xpm2ps . I have
> > few
> > > questions
> > >
> > > - Have any of you ever done this type of plot? If yes, how?
> > > - What parameters for densmap and/or xpm2ps did you use?
> > > - How did you combine the protein and surfactant xpm files into a
> single
> > > one to obtain the same plot as Fig. 4
> > >
> > > Thanks in advance for your help
> > >
> > > St?phane
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --
> > Best regards
> >
> > Wenjuan Jiang
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> --
> Best regards
>
> Wenjuan Jiang
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 24 Oct 2018 13:46:29 -0500
> From: Raji <raji.phy at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Adding residue to .rtp file
> Message-ID:
> <
> CAPoAzqoeTFosam2GYbFH0vbr_4ycdU_NFS23DCcaXvQrC+qsNQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you for your reply. I have few more questions
> 1. Yes, command pdb2gmx continued and generated the topology. The warning
> is about 74 atoms which are from the new added rtp entry. I just want to
> understand more about the warning. I dont find any related information?
> 2. What is the significance of the atom types in the rtp file?
> for example
> CTL3 - carbon of methyl group
> CG331 - Aliphatic C for methyl group
> What is the difference between them and How to choose the right one for
> carbon in alkyl chain?
>
>
> Thanks
> Raji
>
>
> >
> >
> > Message: 1
> > Date: Fri, 19 Oct 2018 18:32:23 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Adding residue to .rtp file
> > Message-ID: <eb75936f-47a3-ce9b-cf0e-2059ee843e4c at vt.edu>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> >
> >
> > On 10/18/18 11:45 AM, Raji wrote:
> > > Hi,
> > >
> > > I have added the modified residue entry in the rtp file and able to
> > > generate to topology and .gro file. but i got this warning when passing
> > the
> > > pdb2gmx command.What is this about?
> > > "WARNING: there were 74 atoms with zero occupancy and 0 atoms with
> > > occupancy unequal to one (out of 160 atoms). Check your pdb
> > file."
> >
> > That warning should not present a problem and pdb2gmx should continue.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> >
> > *******************
> >
>
>
> ------------------------------
>
> --
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> End of gromacs.org_gmx-users Digest, Vol 174, Issue 61
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