AMBER Archive (2007)

Subject: AMBER: DNA on Si surface

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Thu Nov 29 2007 - 17:20:12 CST

Hi I would like to open (load) a Pdb file in amber7.

the file contains DNA on Si surface.

REMARK 4

REMARK 4 APRI COMPLIES WITH FORMAT V. 2.0, 28-NOV-2007

ATOM 1 P A 1 9.689 -14.560 -6.570 1.00 0.00
      P
ATOM 2 O1P A 1 10.801 -14.460 -7.621 1.00 0.00
      O
ATOM 3 O2P A 1 8.367 -14.852 -7.286 1.00 0.00
      O
ATOM 4 O5* A 1 9.580 -13.160 -5.758 1.00 0.00
      O
ATOM 5 O3* A 1 11.142 -10.619 -3.312 1.00 0.00
      O
.
.
.ATOM 697 2H1 ETHL 1C 0.500 -7.542 -14.394 1.00 0.00
       H
ATOM 698 1H2 ETHL 1C -0.008 -6.993 -11.388 1.00 0.00
      H
ATOM 699 2H2 ETHL 1C -0.013 -8.592 -12.136 1.00 0.00
      H
ATOM 700 SI1 XXXX 1I 30.624 17.149 -10.790 1.00 0.00
     Si
ATOM 701 SI2 XXXX 1I 25.330 18.330 -11.051 1.00 0.00
     Si
ATOM 702 SI3 XXXX 1I 20.037 19.510 -11.313 1.00 0.00
     Si
ATOM 703 SI4 XXXX 1I 14.743 20.690 -11.574 1.00 0.00
     Si
ATOM 704 SI5 XXXX 1I 9.449 21.871 -11.836 1.00 0.00
     Si
ATOM 705 SI6 XXXX 1I 4.156 23.051 -12.097 1.00 0.00
     Si
ATOM 706 SI7 XXXX 1I -1.138 24.231 -12.359 1.00 0.00
     Si
...

when i try to view this with edit (using xleap) i see few Si atoms and
they are not connected. If i try and view the pdb file using VMD it
looks fine.

Thank you for your help,
Taufik

Taufik Al-Sarraj wrote:
>>
>> Hi,
>> I have recently started using AMBER7, i worked through some of Ross
>> Walker tutorials. But what i am really interested in is modelling DNA
>> on a Silica surface. i have a couple of questions.
>>
>> 1. how can i draw a lattice structure for Si. say Si(100)
>> 2. is there a force field that can handle both organic (DNA) and
>> inorganic (Si) molecules? i can have the Si atoms fixed if needed?
>>
>> Any hints are much appreciated, Thank you.
>>
>> Taufik
>> Chemical Sensors Group
>> UTM
>
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