[gmx-users] Re: ANTECHAMBER & GAFF

David Mobley dmobley at gmail.com
Tue Oct 2 16:06:56 CEST 2007 

Dechang,

>    With the help of Yang Ye and Mark, I downloaded amb2gmx.pl to transform the topology from AMBER format to
> GROMACS. But the script requires an AMBER installation to work and I didn't have a AMBER package. How can I go on?

Mark pointed out one option -- rethink your choice of force field.

The script relies on an Amber installation basically for convenience:
It's easier (and more robust) to convert Amber to GROMACS using some
of the file formats AMBER can output than directly from the prmtop and
crd files only. However, prmtop and crd files *can* be output by
Antechamber (which is free) without an AMBER installation.

Anyway, that means another option would be for you to rewrite the
script to work just from prmtop and crd files rather than also
requiring the rdparm and modified pdb input it currently requires
(which is where the Amber dependency comes in). This would of course
be a significant amount of work, and no one will do it for you.
However, if you want to do it, I'm happy to help you check your work
by using my Amber installation to ensure we get the same topologies
out of your new version as out of the original version.

Best wishes,
David


>
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> >Today's Topics:
> >
> >   1. Gromacs for Aerosol Particle Agglomeration (Lorenzo Isella)
> >   2. Re: Gromacs for Aerosol Particle Agglomeration (Yang Ye)
> >   3. ANTECHAMBER & GAFF (Dechang Li)
> >   4. Re: ANTECHAMBER & GAFF (Mark Abraham)
> >   5. Re: ANTECHAMBER & GAFF (Yang Ye)
> >   6. Re: Reading XTC files from fortran90 (Jones de Andrade)
> >   7. Re: Reading XTC files from fortran90 (Bert de Groot)
> >
> >
> >----------------------------------------------------------------------
> >
> >Message: 1
> >Date: Sat, 29 Sep 2007 15:13:51 +0200
> >From: Lorenzo Isella <lorenzo.isella at gmail.com>
> >Subject: [gmx-users] Gromacs for Aerosol Particle Agglomeration
> >To: gmx-users at gromacs.org
> >Message-ID: <46FE4F8F.40100 at gmail.com>
> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >Dear All,
> >I am 100% new on this list and to Molecular Dynamics in general.
> >This is what I am interested into (and would like to know if Gromacs is
> >then the right tool).
> >I am not really into biology or chemistry, but rather in aerosol science.
> >I am interested in studying how diesel exhaust aerosol particles,
> >generally carried by a turbulent exhaust flow, collide and, by
> >"sticking" together, give rise to complicated structures (idea of
> >agglomeration).
> >We now leave aside the technicalities (how they stick, what the
> >compenetration depends upon etc.), but first of all I would like to know
> >if Gromacs is the right tool for doing that.
> >Typically, I deal with concentrations around 10^8 particles per cm^3 and
> >I need to follow the evolution of the system for some seconds.
> >The particles carrier-flow is typically turbulent, but collisions are
> >mainly due to Brownian motion (I am thinking about some Langevin dynamics).
> >I have access to a few nodes in a cluster (if that becomes a necessity)
> >but have no experience in running parallel codes.
> >A last (but not least) question: I installed gromacs on my Debian
> >Testing laptop; how do I run the examples/tutorials?
> >Is there any available gromacs code you recommend me to look at for my
> >specific problem or as a good way to learn the ropes?
> >Many thanks
> >
> >Lorenzo
> >
> >
> >
> >
> >------------------------------
> >
> >Message: 2
> >Date: Sat, 29 Sep 2007 21:54:24 +0800
> >From: Yang Ye <leafyoung at yahoo.com>
> >Subject: Re: [gmx-users] Gromacs for Aerosol Particle Agglomeration
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Message-ID: <46FE5910.3080104 at yahoo.com>
> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >On 9/29/2007 9:13 PM, Lorenzo Isella wrote:
> >> Dear All,
> >> I am 100% new on this list and to Molecular Dynamics in general.
> >> This is what I am interested into (and would like to know if Gromacs is
> >> then the right tool).
> >> I am not really into biology or chemistry, but rather in aerosol science.
> >> I am interested in studying how diesel exhaust aerosol particles,
> >> generally carried by a turbulent exhaust flow, collide and, by
> >> "sticking" together, give rise to complicated structures (idea of
> >> agglomeration).
> >> We now leave aside the technicalities (how they stick, what the
> >> compenetration depends upon etc.), but first of all I would like to know
> >> if Gromacs is the right tool for doing that.
> >You may consult the gromacs manual, which is also a good introductory
> >material on the topic of MD. You need to check especially whether the
> >interaction existed in your system can be found in GROMACS' supported
> >inter-particle interaction.
> >> Typically, I deal with concentrations around 10^8 particles per cm^3 and
> >> I need to follow the evolution of the system for some seconds.
> >> The particles carrier-flow is typically turbulent, but collisions are
> >> mainly due to Brownian motion (I am thinking about some Langevin
> >> dynamics).
> >> I have access to a few nodes in a cluster (if that becomes a necessity)
> >> but have no experience in running parallel codes.
> >You can leave this question later.
> >> A last (but not least) question: I installed gromacs on my Debian
> >> Testing laptop; how do I run the examples/tutorials?
> >GROMACS works almost with command-line tools so you need to open the
> >terminal windows to type commands inside them. So get yourself with some
> >basic Linux/Unix commands first if you are no so; then proceed with the
> >tutorial.
> >> Is there any available gromacs code you recommend me to look at for my
> >> specific problem or as a good way to learn the ropes?
> >Check literature. I guess there would be some MD work done on your
> >topic. You may then migrate them to GROMACS by looking at them. You may
> >raise relevant question to this list.
> >
> >However, if you are doing Langevin dynamics of non-atomistic models, you
> >may get easier life with Espresso than GROMACS.
> >www.*espresso*.mpg.de
> >> Many thanks
> >>
> >> Lorenzo
> >>
> >>
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before
> >> posting!
> >> Please don't post (un)subscribe requests to the list. Use the www
> >> interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >
> >
> >
> >------------------------------
> >
> >Message: 3
> >Date: Sat, 29 Sep 2007 22:22:59 +0800
> >From: Dechang Li <li.dc06 at gmail.com>
> >Subject: [gmx-users] ANTECHAMBER & GAFF
> >To: "gmx-users" <gmx-users at gromacs.org>
> >Message-ID: <46fe5fe9.15ec720a.6f09.ffffe26f at mx.google.com>
> >Content-Type: text/plain;      charset="gb2312"
> >
> >Dear gmx-users，
> >     I want to use ANTECHAMBER & GAFF to generate the topology of a small molecular(HIV-1 Protease inhibitor, Nelfinavir) for gromacs.
> >But It seems to be not so simple. Is there anyone who did the similar thing before? Is there any tutorials?
> >
> >
> >
> >With best regards,
> >2007-9-29
> >
> >=========================================
> >Dechang Li, PhD Candidate
> >Department of Engineering Mechanics
> >Tsinghua University
> >Beijing 100084
> >PR China
> >
> >Tel:   +86-10-62773779(O)
> >Email: lidc02 at mails.tsinghua.edu.cn
> >=========================================
> >
> >------------------------------
> >
> >Message: 4
> >Date: Sun, 30 Sep 2007 00:45:13 +1000
> >From: Mark Abraham <Mark.Abraham at anu.edu.au>
> >Subject: Re: [gmx-users] ANTECHAMBER & GAFF
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Message-ID: <46FE64F9.6090308 at anu.edu.au>
> >Content-Type: text/plain; charset=GB2312
> >
> >Dechang Li wrote:
> >> Dear gmx-users，
> >>      I want to use ANTECHAMBER & GAFF to generate the topology of a small molecular(HIV-1 Protease inhibitor, Nelfinavir) for gromacs.
> >> But It seems to be not so simple. Is there anyone who did the similar thing before? Is there any tutorials?
> >
> >http://wiki.gromacs.org/index.php/AMBER
> >
> >Mark
> >
> >
> >------------------------------
> >
> >Message: 5
> >Date: Sat, 29 Sep 2007 22:49:42 +0800
> >From: Yang Ye <leafyoung at yahoo.com>
> >Subject: Re: [gmx-users] ANTECHAMBER & GAFF
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Message-ID: <46FE6606.70805 at yahoo.com>
> >Content-Type: text/plain; charset=GB2312
> >
> >The antechamber's website has a tutorial
> >http://amber.scripps.edu/antechamber/antechamber.html
> >
> >For faster results, you can use AM1/BCC for partial charge
> >determination; while keep Guassian's version running alongside.
> >
> >Later you will need to transform the topology from AMBER format to
> >GROMACS. The amb2gmx.pl from E.J. Sorin shall help
> >(http://chemistry.csulb.edu/ffamber/tools.html).
> >
> >Regards,
> >Yang Ye
> >
> >On 9/29/2007 10:22 PM, Dechang Li wrote:
> >> Dear gmx-users，
> >>      I want to use ANTECHAMBER & GAFF to generate the topology of a small molecular(HIV-1 Protease inhibitor, Nelfinavir) for gromacs.
> >> But It seems to be not so simple. Is there anyone who did the similar thing before? Is there any tutorials?
> >>
> >>
> >>
> >> With best regards,
> >> 2007-9-29
> >>
> >> =========================================
> >> Dechang Li, PhD Candidate
> >> Department of Engineering Mechanics
> >> Tsinghua University
> >> Beijing 100084
> >> PR China
> >>
> >> Tel:   +86-10-62773779(O)
> >> Email: lidc02 at mails.tsinghua.edu.cn
> >> =========================================
> >>
> >> ------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> gmx-users mailing list    gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
> >------------------------------
> >
> >Message: 6
> >Date: Sat, 29 Sep 2007 13:53:50 -0300
> >From: "Jones de Andrade" <johannesrs at gmail.com>
> >Subject: Re: [gmx-users] Reading XTC files from fortran90
> >To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >Message-ID:
> >       <54e4355e0709290953w38648a2ek3832e4f96755066a at mail.gmail.com>
> >Content-Type: text/plain; charset="iso-8859-1"
> >
> >Hi Bert.
> >
> >Thank you for the prompt answer.
> >
> >Just did as instructed, but got the following:
> >
> >CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90
> >-L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c
> >IPO link: can not find -lxrdf
> >ifort: error: problem during multi-file optimization compilation (code 1)
> >
> >Looks better, in the sense that the number of error messages was reduced.
> >But still doesn't accept to link to the xrdf library.
> >
> >Tried that with and without re-make of the library (strange fact that the
> >SGI arch is to be used in linux) and also tried to say -llibxrdf instead of
> >-lxrdf. Nothing worked.
> >
> >Have you or someone come across such an error before? Any clue of what can
> >possibly be going wrong?
> >
> >Thanks a lot in advance...
> >
> >Sincerally yours,
> >
> >Jones
> >
> >On 9/29/07, Bert de Groot <bgroot at gwdg.de> wrote:
> >>
> >> Hi,
> >>
> >> try:
> >>
> >> download
> >> http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz
> >>
> >> (and optionally issue a 'make' in the xtc directory after unpacking)
> >>
> >> in the linking stage, use something like
> >>
> >> ifort -blabla -lxdrf -L/wherever/xtc -lg2c
> >>
> >> your smalll test code looks OK apart from the fact that I don't know what
> >> happens if you read&write from the same file.
> >>
> >> Bert
> >>
> >-------------- next part --------------
> >An HTML attachment was scrubbed...
> >URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20070929/45084c42/attachment-0001.html
> >
> >------------------------------
> >
> >Message: 7
> >Date: Sat, 29 Sep 2007 22:59:06 +0200 (MEST)
> >From: Bert de Groot <bgroot at gwdg.de>
> >Subject: Re: [gmx-users] Reading XTC files from fortran90
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Message-ID: <Pine.OSF.4.58.0709292254310.58090 at gwdu71.gwdg.de>
> >Content-Type: TEXT/PLAIN; charset=US-ASCII
> >
> >On Sat, 29 Sep 2007, Jones de Andrade wrote:
> >
> >> Hi Bert.
> >>
> >> Thank you for the prompt answer.
> >>
> >> Just did as instructed, but got the following:
> >>
> >> CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90
> >> -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c
> >> IPO link: can not find -lxrdf
> >
> >
> >well, apparently the path you specify with -L does not contain a
> >libxdrf.a
> >
> >the way you called it the compiler expects it to be located here:
> >/home/johannes/src/own/B/9/xtc/xtc/libxdrf.a
> >
> >also, IIRC, the xtcio stuff is already linked into the libxdrf.a, so no
> >need to include it again.
> >
> >
> >> ifort: error: problem during multi-file optimization compilation (code 1)
> >>
> >> Looks better, in the sense that the number of error messages was reduced.
> >> But still doesn't accept to link to the xrdf library.
> >>
> >> Tried that with and without re-make of the library (strange fact that the
> >> SGI arch is to be used in linux) and also tried to say -llibxrdf instead of
> >> -lxrdf. Nothing worked.
> >>
> >> Have you or someone come across such an error before? Any clue of what can
> >> possibly be going wrong?
> >>
> >> Thanks a lot in advance...
> >>
> >> Sincerally yours,
> >>
> >> Jones
> >>
> >> On 9/29/07, Bert de Groot <bgroot at gwdg.de> wrote:
> >> >
> >> > Hi,
> >> >
> >> > try:
> >> >
> >> > download
> >> > http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz
> >> >
> >> > (and optionally issue a 'make' in the xtc directory after unpacking)
> >> >
> >> > in the linking stage, use something like
> >> >
> >> > ifort -blabla -lxdrf -L/wherever/xtc -lg2c
> >> >
> >> > your smalll test code looks OK apart from the fact that I don't know what
> >> > happens if you read&write from the same file.
> >> >
> >> > Bert
> >> >
> >>
> >
> >
> >Bert
> >
> >
> >
> >________________________________________________
> >Bert de Groot, PhD
> >
> >Max Planck Institute for Biophysical Chemistry
> >Computational biomolecular dynamics group
> >Am Fassberg 11
> >37077 Goettingen, Germany
> >
> >tel: +49-551-2012308, fax: +49-551-2012302
> >
> >http://www.mpibpc.gwdg.de/groups/de_groot
> >
> >
> >------------------------------
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
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> >
> >End of gmx-users Digest, Vol 41, Issue 94
> >*****************************************
>
>
>
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