Dear gmx-users, 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?
>Send gmx-users mailing list submissions to > [email protected] > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users >or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > >You can reach the person managing the list at > [EMAIL PROTECTED] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gmx-users digest..." > > >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 <[EMAIL PROTECTED]> >Subject: [gmx-users] Gromacs for Aerosol Particle Agglomeration >To: [email protected] >Message-ID: <[EMAIL PROTECTED]> >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 <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Gromacs for Aerosol Particle Agglomeration >To: Discussion list for GROMACS users <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >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 [email protected] >> 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 [EMAIL PROTECTED] >> 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 <[EMAIL PROTECTED]> >Subject: [gmx-users] ANTECHAMBER & GAFF >To: "gmx-users" <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >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: [EMAIL PROTECTED] >========================================= > >------------------------------ > >Message: 4 >Date: Sun, 30 Sep 2007 00:45:13 +1000 >From: Mark Abraham <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] ANTECHAMBER & GAFF >To: Discussion list for GROMACS users <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >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 <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] ANTECHAMBER & GAFF >To: Discussion list for GROMACS users <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >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: [EMAIL PROTECTED] >> ========================================= >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [EMAIL PROTECTED] >> 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" <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Reading XTC files from fortran90 >To: "Discussion list for GROMACS users" <[email protected]> >Message-ID: > <[EMAIL PROTECTED]> >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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Reading XTC files from fortran90 >To: Discussion list for GROMACS users <[email protected]> >Message-ID: <[EMAIL PROTECTED]> >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 <[EMAIL PROTECTED]> 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 >[email protected] >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! > >End of gmx-users Digest, Vol 41, Issue 94 >*****************************************
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