Dear Justin:
On Wed, Mar 4, 2009 at 10:04 AM, Justin A. Lemkul <[email protected]> wrote: > > > Tree wrote: > >> Dear Justin: >> >> >> Thank you for your answer!! >> Yes, I found there is already a bond defined for CT and CT, meanwhile I am >> waiting response from gmx-uses. I deleted mine! >> >> To confirm, I cannot avoid to ask you a question again. >> So, please let me explain... >> Sections [ bonds ], [pairs], [angles] and etc. in the "topol.top" show the >> information on what interaction (and how) exist among atoms in those >> sections. >> Real potential values are interpreted (assigned) when I run "grompp" to >> get "tpr" file. >> --- Is this right? >> > > Yes. > > >> If this is right, I do not understand why I am not able to have new >> "topol_new.top" file when I use "-pp topol_new.top" with "grompp". >> There is no error message... >> > > It isn't produced? It is produced. However, it seems having ALL the informations from '.atp', 'bon.itp' and 'nb.itp'... Since I guessed that I would get a "processed" topology file having information, which was blank in the original topology file, this looks pretty weird... > > > --- What does the "-pp" option generate when doing grompp-? >> >> > The -pp option gives you a "processed" topology, explicitly showing every > parameter that grompp assembled. Yes... That is what I understood... Since I do not think I had an appropriate "processed" topology, I guessed that there may be different meaning. Thank you for your confirmation. > > > Regarding the assignment of opls_xxx to atom type is, I think, well >> described in the file, "csoplsaanb.itp". >> >> > Is that some sort of modified form of ffoplsaanb.itp? Often times a more > detailed explanation is found in the .atp file for the corresponding force > field. > > -Justin > > Thank you again! >> >> >> Sincerely >> >> C Kim >> >> On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Tree wrote: >> >> Dear All: >> >> >> *[1 - Situation]* >> I am trying to define "stretch" between two bonded atoms (for >> example, in my system PE (polyethylene), C-C). >> >> *[2 - ffoplsaa.rtp file]* >> In ffoplsaa.rtp file, I assigned C1 > opls_136 >> C2 > opls_135 >> This can be done by my own idea, so it does not bother anything. >> And totally okay. >> >> *[3 - opls_xxx and atom type]* >> I found that the oplsaa interpret those "opls_xxx" atoms to atom >> types (which are in ffoplsaabon.itp file) as follows, >> opls_136 > CT >> opls_135 > CT. >> >> ( from a file containing opls_136 CT 6 12.01100 >> -0.120 A 3.50000e-01 2.76144e-01 >> opls_137 CT 6 12.01100 -0.060 A 3.50000e-01 >> 2.76144e-01 >> ) >> >> *[4 - ffoplsaabon.itp]* >> Based on the information in the section [2] and [3] above, I >> added following two sentences in the ffoplsaabon.itp file. >> >> [ bondtypes ] >> ; i j func b0 kb >> CT CT 1 0.14900 334720.0 ; >> >> >> There is already a CT-CT bond defined in ffoplsaabon.itp: >> >> CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file >> >> If you don't want those parameters, make sure you comment out that >> line so you know which parameters you are actually using! >> >> *[5 - pdb2gmx result]* >> >> Until the section [4], I have new ffoplsaabon.itp file, so I ran >> pdb2gmx for my PE system. >> After that, when I looked at the topology file (e.g. topol.top), >> I could not find any information in the [ bonds ] section (after >> the [ atoms ] section). >> In other words, topol.top shows nothing in [ bonds ] section. >> [ bonds ] >> ; ai aj funct c0 c1 c2 >> c3 >> 1 2 1 >> >> >> It's not showing nothing. Atoms 1 and 2 are bonded together. As >> long as there are parameters defined in ffoplsaabon.itp, then grompp >> will interpret the topology correctly. If grompp fails, then you >> have identified a problem. >> >> *[6 - Question!]* >> >> I think my mistake came from section [3] or [4]. >> (1) Would you please let me know what I did wrong...? >> >> >> Nothing so far that I can see (aside from potentially duplicating >> parameters). >> >> >> (2) If someone is familiar with defining stretch, angle, >> dihedral and torsion in ffoplsaabon.itp, would you please give >> me an idea on how-to? >> >> >> How do you define "stretch"? The force constant for how much the >> bond length can deviate? Otherwise, all bonded parameters are >> assigned by pdb2gmx as long as all atom types are defined. >> >> >> (3) Would you please summarize how the gromacs maps opls_xxx >> with atom type (C, CT... etc)? >> >> >> Read ffoplsaa.atp. >> >> -Justin >> >> *[7 - Thank you!]* >> >> Thank you so much your participation and help!!! >> >> >> Sincerely, >> >> Kim >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 >
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