AMBER Archive (2005)

Subject: Re: AMBER: question about loadiing pdb file of a molecule complex

From: Chutintorn Punwong (punwong_at_uiuc.edu)
Date: Fri May 27 2005 - 17:07:52 CDT

The first ATOM number of MAA should be 45 and so on to 56
Chutintorn

---- Original message ----
>Date: Fri, 27 May 2005 17:39:28 -0400
>From: gtg549i_at_mail.gatech.edu
>Subject: AMBER: question about loadiing pdb file of a
molecule complex
>To: amber_at_scripps.edu
>
>I want to study the H-bonding interaction of two molecules.
The following is
>what i did:
>1. download 3D molecule of estradiol and methacrylic acid
from SciFinder, save
>it as pdb files.
>2. With Amber 8, use antechamber, parmchk, and xleap to
modify the pdb file,
>save.
>3. Open the modified pdb files in ViewLite and bring them to
proximity for
>H-bond interaction, save the file as "complex.pdb",the two
molecules were
>named as "BE2" and "MAA". here is the file looks like:
>
>ATOM 1 C7 BE2 1 0.035 1.199 -0.000 1.00
 0.00
>ATOM 2 C10 BE2 1 0.872 2.543 -0.032 1.00
 0.00
>...
>ATOM 44 H86 BE2 1 -6.124 -2.328 -0.042 1.00
 0.00
>TER
>ENDMDL
>TER
>ATOM 1 C3 MAA 2 3.776 7.634 0.370 1.00
 0.00
>ATOM 2 H12 MAA 2 4.741 7.876 0.262 1.00
 0.00
>...
>ATOM 12 O5 MAA 2 1.280 6.280 0.431 1.00
 0.00
>TER
>ENDMDL
>
>4.When i try to load it into xleap, the following messages
come out:
>!FATAL ERROR----------------------------------------
>!FATAL: In file [chirality.c], line 142
>!FATAL: Message: Atom named C1 from MAA did not match !
>!
>!ABORTING.
>
>I wonder how to make this pdb file recognized by xleap. I can
load the pdb
>file of single molecule but not the complex. thanks!
>
>
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