[gmx-users] How to define "stretch" in ffoplsaabon.itp ?
tree.csc at gmail.com
Wed Mar 4 16:01:11 CET 2009
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
Real potential values are interpreted (assigned) when I run "grompp" to get
--- Is this right?
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...
--- What does the "-pp" option generate when doing grompp-?
Regarding the assignment of opls_xxx to atom type is, I think, well
described in the file, "csoplsaanb.itp".
Thank you again!
On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul <jalemkul at vt.edu> 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
>> *[4 - ffoplsaabon.itp]*
>> Based on the information in the section  and  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 , 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 ]
>> In other words, topol.top shows nothing in [ bonds ] section.
>> [ bonds ]
>> ; ai aj funct c0 c1 c2
>> 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
> *[6 - Question!]*
>> I think my mistake came from section  or .
>> (1) Would you please let me know what I did wrong...?
> Nothing so far that I can see (aside from potentially duplicating
> (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.
> *[7 - Thank you!]*
>> Thank you so much your participation and help!!!
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before
>> 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
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users