Hi Martiniano
Apologies, for some reason I missed your mail sent to dbt.query.gmail.com.
As you said, with PDB file you see TER cards and thus there will be no
bonds. To avoid this, use mol2 (saved with top2mol2) which works fine. DBT
(Dendrimer Builder Toolkit) itself uses top2mol2 and the mol2 file can be
used directly without modifications. Also you can load mol2 file directly
and then do this (also as Daniel suggested, Thanks)
G4=loadmol2 L4.mol2
saveamberparm G4 G4.prmtop G4.inpcrd
In this case do not save as PDB or use it to create prmtop/inpcrd files.
There will be no bonds. In such case dendrimer residues will fall apart
during simulations.
Also the head and tail atoms are defined by 'set tail' and 'set head'
options while joining residues step by step by DBT and finally a mol2 file
is generated which has all bond info and atom type info.
If you have any further queries related to DBT please let me know. Also if
you want to discuss something offlist please send mail to
dbt.query.gmail.com but discussing here will be helpful for others as well
in future.
This reminds me something here that I would like to ask. I am just
wondering why top2mol2 functionality has been removed with new Ambertools?
best regards,
Vishal
On Sun, Oct 12, 2014 at 6:14 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Sun, Oct 12, 2014 at 10:59 AM, Martiniano Bello Ramirez
> <bellomartini.gmail.com> wrote:
> > I would like to know if some modifications have to be performed after
> > obtaining the .mol2 by dendrimer builder? Furthermore, I have observed
> that
> > after obtaining the .pdb file from the.mol2 file, there are ter cards
> after
> > each aa, bbb and ccc subunits, which may cause confusion to sander and
> > pmend. I am using the following instructions to generate my .prmtop and
> > .crd:
> >
> > tleap
> > source leaprc.gaff
> > source leaprc.ff99SB
> > loadoff pamam_basic_EDA.lib
> > G4=loadmol2 L4.mol2
> > Savepdb G4 G4.pdb
>
> I'm guessing there is a 'saveamberparm' command that was used to
> generate the actual topology/restart you used in your simulation that
> you haven't listed here?
>
> You can use parmed.py or cpptraj to check if there are actually bonds
> between your subunits in your Amber topology file (use 'printbonds
> <mask>' where <mask> contains the atoms that should be bonded). If
> there really aren't bonds, I suspect the problem may be with the
> residue units in 'pamam_basic_EDA.lib' not having defined
> connect0/connect1 (head/tail) atoms, hence the subunits aren't being
> linked. However, without seeing your topology file, the lib file, or
> the exact output from tleap I can only speculate.
>
> -Dan
>
> >
> >
> >
> > Best wishes,
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*****
*regards;Vishal Maingi*
*Dendrimer Builder Toolkit (DBT)*
\I/
>-|-<
/I\
*http://www.physics.iisc.ernet.in/~maiti/dbt/home.html
<http://www.physics.iisc.ernet.in/%7Emaiti/dbt/home.html>*
*****
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 13 2014 - 09:00:02 PDT
