Re: [AMBER] dendrimer-query

From: Daniel Roe <>
Date: Sun, 12 Oct 2014 11:14:57 -0600


On Sun, Oct 12, 2014 at 10:59 AM, Martiniano Bello Ramirez
<> 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 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.


> Best wishes,
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Oct 12 2014 - 10:30:02 PDT
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