Hi,
Thanks Daniel, I had a quick check it seems working fine.
kind regards,
Vishal
On Tue, Oct 14, 2014 at 9:49 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Oct 13, 2014 at 9:33 AM, Vishal Maingi
> <maingi.ambquery.gmail.com> wrote:
> >
> > This reminds me something here that I would like to ask. I am just
> > wondering why top2mol2 functionality has been removed with new
> Ambertools?
>
> You can use cpptraj to generate a mol2 using Amber topology and
> restart/trajectory:
>
> cpptraj -p top.parm7 -y mymol.rst7 -x mymol.mol2
>
> I think the results should be similar to (if not the same as)
> top2mol2. Let me know if this is not the case for you.
>
> -Dan
>
> >
> > 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
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> > 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>*
*****
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Received on Thu Oct 16 2014 - 08:30:02 PDT
