[gmx-users] Re: ANTECHAMBER & GAFF

[Dechang Li]

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?



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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
>>
>>
>> _______________________________________________
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>> Please search the archive at http://www.gromacs.org/search before 
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>>
>
>
>
>------------------------------
>
>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
>>
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>------------------------------
>
>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
>
>
>------------------------------
>
>_______________________________________________
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>End of gmx-users Digest, Vol 41, Issue 94
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