AMBER Archive (2007)

Subject: AMBER: loading a crystal PDB file

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Dec 12 2007 - 19:33:36 CST

Hi,
I have a pdb file that looks like this

REMARK Materials Studio PDB file
REMARK Created: Wed Dec 12 18:20:24 Pacific Standard Time 2007
CRYST1 54.052 49.130 13.634 90.00 90.00 90.00 P1
ATOM 1 OX1 MOL 2 1.760 0.299 1.157 1.00 0.00
      O
ATOM 2 OX1 MOL 2 3.116 3.831 2.959 1.00 0.00
      O
ATOM 3 OX1 MOL 2 3.634 0.783 4.761 1.00 0.00
      O
ATOM 4 OX1 MOL 2 1.139 1.375 4.248 1.00 0.00
      O
ATOM 5 OX1 MOL 2 0.621 3.240 2.446 1.00 0.00
      O
ATOM 6 OX1 MOL 2 2.495 2.755 0.644 1.00 0.00
      O
ATOM 7 SI1 MOL 2 2.000 3.758 1.802 1.00 0.00
     Si
ATOM 8 SI1 MOL 2 0.000 2.310 3.603 1.00 0.00
     Si
ATOM 9 SI1 MOL 2 2.255 1.302 -0.000 1.00 0.00
     Si
ATOM 10 OX1 MOL 2 1.760 0.299 6.562 1.00 0.00
      O

i picked the first 10 atoms, my file contains 800 atoms. Amber can
recognize one oxygen and one Si atoms only. is there a way to load this
in xleap using loadpdb command and still be able to see all 800 atoms?
it is a little unreasonable to modify the name of every atom using Vi.

Any help is greatly appreciated,
Taufik

P.S. i am using Amber 7

David A. Case wrote:
> On Wed, Dec 12, 2007, Campbell, Patrick wrote:
>>
>> I am a student and I have recently started the usage of AMBER for protein
>> optimization. The question that I have might have a straightforward response
>> so do bear with me.
>>
>> I have created an input file (run.com) for the optimization of my protein.
>>
>> My PDB protein is saved in my working directory under the name LTR. I have
>> also saved the input file (shown above) under the name run.com - I thus have
>> two files in my working directory.
>>
>> I would like to optimize the PDB file and would like to know how the link
>> between the input file and the PDB file is made.
>
> Sounds like you need to start with the tutorials; there are intermediate
> steps to take between having a pdb file and running sander.
>
> http://amber.scripps.edu/tutorials
>
> ...dac
>
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