[AMBER] dendrimer-query

From: Martiniano Bello Ramirez <bellomartini.gmail.com>
Date: Sun, 12 Oct 2014 11:59:42 -0500

Dear Amber users,

At the present, I am performing MD simulations with some dendrimers
constructed using dendrimers builder Toolkit. By the way everything goes
good during the preparation, equilibration and MD simulations. However,
when I try to obtain snapshots from different times of the trajectory, the
dendrimer looks as if it had not covalent bonds between the aa, bbb and ccc
subunits constituting the dendrimers. I am using the following instructions
with ptraj to remove periodicity:

trajin prod.mdcrd 1 5000 10

center :1-125 mass origin

image origin center familiar

strip :Na+,WAT

trajout prod-total.binpos binpos

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


source leaprc.gaff

source leaprc.ff99SB

loadoff pamam_basic_EDA.lib

G4=loadmol2 L4.mol2

Savepdb G4 G4.pdb

 Best wishes,
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Received on Sun Oct 12 2014 - 10:00:08 PDT
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