Content-Type: multipart/alternative; boundary="_58a92e4a-fbd3-4799-97a7-3797de2bf42f_" --_58a92e4a-fbd3-4799-97a7-3797de2bf42f_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello David=2C how do you do?=20 I'm so sorry another time to bother you with my question=2C but right now I= guess that my last message ending up in misunderstanding. Let's me tell y= ou=2C my main interest with Advogadro is making molecules and try to optimi= zing them at the same time=2C but I do not really know one way to make mole= cular dynamics using Advogadro=2C so for that reason I have been working wi= th other program called=2C GROMACS=2C which in it=2C I have to introduce a = document with the information of all parameter about atoms (bonds=2C angles= =2C torsion=2C van der Waals=2Cetc ) beside the file.pdb (molecule). =20 According with the link http://openbabel.org/wiki/OBForceFieldMMFF94 that y= ou kindly sent me=2C I want to know which are the constant that Avogadro us= es to make the optimization=2C I mean=2C the constant related with MMFF94 t= his force field=2C how it identify which one is which one????? If I can= get this kind of information=2C I will can transform the formulas of MMFF9= 4 and the constant to other Force Field from then OPLS library. =20 Perhaps Avogadro generates a file with a specific atoms parameter that it u= ses to optimize with MMFF94. Let's me be more exactly=2C how can I get the parameter of the MMFF94 corre= sponding to the adjunct molecule??? To make the optimization?=20 Thanks so much=2C I will be absolutely grateful with your answer.=20 =20 > From: loniedavid@gmail.com > Date: Tue=2C 24 Jan 2012 10:05:09 -0500 > Subject: Re: avogadro question > To: davidea86_30@hotmail.com > CC: avogadro-discuss@lists.sourceforge.net >=20 > Hi David=2C >=20 > On Mon=2C Jan 23=2C 2012 at 4:56 PM=2C David Velasco Villamizar > wrote: > > Let's me tell you that your answer was absolutely useful to my research= and > > it helped me to have a new landscape of Avogadro Program=2C but right n= ow I'm > > totally interested to find a way in Avogadro to generate a file or and > > option where I can get the information related with the atomic paramete= r > > that it used to make the optimization(the parameter of the Force Field = and > > what kind of atom are evolving)=2C I mean=2C is there a way to generate= from > > Avogadro a topology file of the molecule over a determined force field? >=20 > I've cc'd this email to the avogadro discussion mailing list=2C someone > there may be more familiar with what you need. >=20 > I'm not sure what you mean by a "topology file"=2C and how it would > relate to the forcefield? Could you provide an example of what such a > file would contain? >=20 > You've mentioned bond properties (angles=2C torsions=2C etc) -- perhaps > the "report" format would provide what you are looking for. Open your > molecule in Avogadro and select "File > Save as". Save it with a > ".report" extension=2C e.g. "c60-opt.report". This will produce a text > file that contains a distance matrix=2C bond angles=2C and torsion angles= . > See the attached for an example. There are many more formats that can > be used that may be useful=2C like the "gzmat" format which produces a > zmatrix. A full list of supported extensions and their descriptions is > here: >=20 > http://openbabel.org/docs/dev/FileFormats/Overview.html >=20 > If you're on linux=2C you can also perform these conversions on the > command line with the "babel" command: >=20 > babel -i[input extension] [inputfile] -o[output extension] [outputfile] >=20 > So for the pdb file you sent=2C >=20 > babel -ipdb c60-opt.pdb -oreport c60-opt.report >=20 > will produce the c60-opt.report file. >=20 > Dave >=20 > >> From: loniedavid@gmail.com > >> Date: Mon=2C 23 Jan 2012 14:36:36 -0500 > >> Subject: Re: avogadro question > >> To: davidea86_30@hotmail.com > >> > >> Hi David=2C > >> > >> The energy minimization / geometry optimization feature in Avogadro > >> uses a molecular mechanics forcefield to evaluate the energy of the > >> molecule and search for locally optimal geometries. Depending on which > >> forcefield is used (Avogadro supports several=3B GAFF=2C Ghemical=2C M= MFF94=2C > >> UFF...)=2C the formulas and parameters used in the energy calculations > >> are linked to or provided on the OpenBabel wiki: > >> > >> http://openbabel.org/wiki/Molecular_mechanics > >> http://openbabel.org/wiki/OBForceFieldGhemical > >> http://openbabel.org/wiki/OBForceFieldMMFF94 > >> http://openbabel.org/wiki/OBForceFieldUFF > >> > >> If you just want to measure the optimized bond lengths=2C angles=2C > >> torsions=2C etc=2C the "Measure" tool will help with this. The Avogadr= o > >> wiki provides more information on the use of the tool: > >> > >> http://avogadro.openmolecules.net/wiki/Category:Tools > >> > >> Hope this helps=2C > >> > >> Dave > >> > >> On Mon=2C Jan 23=2C 2012 at 6:50 AM=2C David Velasco Villamizar > >> wrote: > >> > Hello David=2C how do you do? > >> > > >> > Let's me ask you something=2C but first of all a little introduce of > >> > myself=2C > >> > I'm David Velasco V. I have been working in my research project in t= he > >> > Institute of Physics=2C University of Santa Catarina=2C Brazil. Actu= ally > >> > I've > >> > been present some problems related with some calculation of molecule= s=2C > >> > more > >> > exactly P3HT/C60=2C which my interest is to get a right energy > >> > optimization > >> > (geometry with minimum of energy) but I haven't got a right idea abo= ut > >> > the > >> > atoms' parameter that Avogadro uses to do it=2C that means=2C what i= s the > >> > length > >> > of bounding? angles between atoms? and torsion angles between four > >> > atoms? > >> > partial charge? If I can subtract this kind of information from the > >> > Avogadro's program=2C I will can do my next steep rightly in molecul= ar > >> > dynamics with other program and use it to organic solar cells resear= ch. > >> > > >> > Let's me know you answer=2C > >> > > >> > Before hand=2C thanks so much! > >> > > >> > David! > >> > = --_58a92e4a-fbd3-4799-97a7-3797de2bf42f_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello David=2C how do you do?

I'm so sorry another time to bother y= ou with my question=2C but right now I guess that my last message ending up= in misunderstanding. =3B Let's me tell you=2C my main interest with Ad= vogadro is making molecules and try to optimizing them at the same time=2C = but I do not really know one way to make molecular dynamics using Advogadro= =2C so for that reason I have been working with other program called=2C GRO= MACS=2C which in it=2C I have to introduce a document with the information = of all parameter about atoms (bonds=2C angles=2C torsion=2C van der Waals= =2Cetc ) beside the file.pdb (molecule). =3B

According with the= link http://openbabel.org/wik= i/OBForceFieldMMFF94 that you kindly sent me=2C I want to know which ar= e the constant that Avogadro uses to make the optimization=2C I mean=2C the= constant related with MMFF94 this force field=2C how it identify which one= is which one?????  =3B  =3B If I can get this kind of information= =2C I will can transform the formulas of MMFF94 and the constant to other F= orce Field from then OPLS library.  =3B =3B

Perhaps Avogadr= o generates a file with a specific atoms parameter that it uses to optimize= with MMFF94.

Let's me be more exactly=2C how can I get the paramete= r of the MMFF94 corresponding to the adjunct molecule??? To make the optimi= zation?


Thanks so much=2C I will be absolutely grateful with yo= ur answer.

 =3B


>=3B From: loniedavid@gmail.com
>=3B Date: Tue=2C 24 Jan = 2012 10:05:09 -0500
>=3B Subject: Re: avogadro question
>=3B To: = davidea86_30@hotmail.com
>=3B CC: avogadro-discuss@lists.sourceforge.n= et
>=3B
>=3B Hi David=2C
>=3B
>=3B On Mon=2C Jan 23= =2C 2012 at 4:56 PM=2C David Velasco Villamizar
>=3B <=3Bdavidea86_3= 0@hotmail.com>=3B wrote:
>=3B >=3B Let's me tell you that your ans= wer was absolutely useful to my research and
>=3B >=3B it helped me = to have a new landscape of Avogadro Program=2C but right now I'm
>=3B = >=3B totally interested to find a way in Avogadro to generate a file or a= nd
>=3B >=3B option where I can get the information related with the= atomic parameter
>=3B >=3B that it used to make the optimization(th= e parameter of the Force Field and
>=3B >=3B what kind of atom are e= volving)=2C I mean=2C is there a way to generate from
>=3B >=3B Avog= adro a topology file of the molecule over a determined force field?
>= =3B
>=3B I've cc'd this email to the avogadro discussion mailing list= =2C someone
>=3B there may be more familiar with what you need.
>= =3B
>=3B I'm not sure what you mean by a "topology file"=2C and how i= t would
>=3B relate to the forcefield? Could you provide an example of= what such a
>=3B file would contain?
>=3B
>=3B You've ment= ioned bond properties (angles=2C torsions=2C etc) -- perhaps
>=3B the = "report" format would provide what you are looking for. Open your
>=3B= molecule in Avogadro and select "File >=3B Save as". Save it with a
&= gt=3B ".report" extension=2C e.g. "c60-opt.report". This will produce a tex= t
>=3B file that contains a distance matrix=2C bond angles=2C and tors= ion angles.
>=3B See the attached for an example. There are many more = formats that can
>=3B be used that may be useful=2C like the "gzmat" f= ormat which produces a
>=3B zmatrix. A full list of supported extensio= ns and their descriptions is
>=3B here:
>=3B
>=3B http://op= enbabel.org/docs/dev/FileFormats/Overview.html
>=3B
>=3B If you'= re on linux=2C you can also perform these conversions on the
>=3B comm= and line with the "babel" command:
>=3B
>=3B babel -i[input exte= nsion] [inputfile] -o[output extension] [outputfile]
>=3B
>=3B S= o for the pdb file you sent=2C
>=3B
>=3B babel -ipdb c60-opt.pdb= -oreport c60-opt.report
>=3B
>=3B will produce the c60-opt.repo= rt file.
>=3B
>=3B Dave
>=3B
>=3B >=3B>=3B From: = loniedavid@gmail.com
>=3B >=3B>=3B Date: Mon=2C 23 Jan 2012 14:36:= 36 -0500
>=3B >=3B>=3B Subject: Re: avogadro question
>=3B &g= t=3B>=3B To: davidea86_30@hotmail.com
>=3B >=3B>=3B
>=3B &g= t=3B>=3B Hi David=2C
>=3B >=3B>=3B
>=3B >=3B>=3B The en= ergy minimization / geometry optimization feature in Avogadro
>=3B >= =3B>=3B uses a molecular mechanics forcefield to evaluate the energy of t= he
>=3B >=3B>=3B molecule and search for locally optimal geometrie= s. Depending on which
>=3B >=3B>=3B forcefield is used (Avogadro s= upports several=3B GAFF=2C Ghemical=2C MMFF94=2C
>=3B >=3B>=3B UFF= ...)=2C the formulas and parameters used in the energy calculations
>= =3B >=3B>=3B are linked to or provided on the OpenBabel wiki:
>=3B= >=3B>=3B
>=3B >=3B>=3B http://openbabel.org/wiki/Molecular_me= chanics
>=3B >=3B>=3B http://openbabel.org/wiki/OBForceFieldGhemic= al
>=3B >=3B>=3B http://openbabel.org/wiki/OBForceFieldMMFF94
&= gt=3B >=3B>=3B http://openbabel.org/wiki/OBForceFieldUFF
>=3B >= =3B>=3B
>=3B >=3B>=3B If you just want to measure the optimized = bond lengths=2C angles=2C
>=3B >=3B>=3B torsions=2C etc=2C the "Me= asure" tool will help with this. The Avogadro
>=3B >=3B>=3B wiki p= rovides more information on the use of the tool:
>=3B >=3B>=3B
= >=3B >=3B>=3B http://avogadro.openmolecules.net/wiki/Category:Tools>=3B >=3B>=3B
>=3B >=3B>=3B Hope this helps=2C
>=3B &= gt=3B>=3B
>=3B >=3B>=3B Dave
>=3B >=3B>=3B
>=3B &g= t=3B>=3B On Mon=2C Jan 23=2C 2012 at 6:50 AM=2C David Velasco Villamizar<= br>>=3B >=3B>=3B <=3Bdavidea86_30@hotmail.com>=3B wrote:
>= =3B >=3B>=3B >=3B Hello David=2C how do you do?
>=3B >=3B>= =3B >=3B
>=3B >=3B>=3B >=3B Let's me ask you something=2C but = first of all a little introduce of
>=3B >=3B>=3B >=3B myself=2C<= br>>=3B >=3B>=3B >=3B I'm David Velasco V. I have been working in m= y research project in the
>=3B >=3B>=3B >=3B Institute of Physic= s=2C University of Santa Catarina=2C Brazil. Actually
>=3B >=3B>= =3B >=3B I've
>=3B >=3B>=3B >=3B been present some problems re= lated with some calculation of molecules=2C
>=3B >=3B>=3B >=3B m= ore
>=3B >=3B>=3B >=3B exactly P3HT/C60=2C which my interest is = to get a right energy
>=3B >=3B>=3B >=3B optimization
>=3B = >=3B>=3B >=3B (geometry with minimum of energy) but I haven't got a r= ight idea about
>=3B >=3B>=3B >=3B the
>=3B >=3B>=3B &g= t=3B atoms' parameter that Avogadro uses to do it=2C that means=2C what is = the
>=3B >=3B>=3B >=3B length
>=3B >=3B>=3B >=3B of b= ounding? angles between atoms? and torsion angles between four
>=3B &g= t=3B>=3B >=3B atoms?
>=3B >=3B>=3B >=3B partial charge? If I= can subtract this kind of information from the
>=3B >=3B>=3B >= =3B Avogadro's program=2C I will can do my next steep rightly in molecular<= br>>=3B >=3B>=3B >=3B dynamics with other program and use it to org= anic solar cells research.
>=3B >=3B>=3B >=3B
>=3B >=3B&g= t=3B >=3B Let's me know you answer=2C
>=3B >=3B>=3B >=3B
&g= t=3B >=3B>=3B >=3B Before hand=2C thanks so much!
>=3B >=3B>= =3B >=3B
>=3B >=3B>=3B >=3B David!
>=3B >=3B>=3B >= =3B
= --_58a92e4a-fbd3-4799-97a7-3797de2bf42f_--