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>*
> *****
> _______________________________________________
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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)
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Received on Tue Oct 14 2014 - 14:00:03 PDT
