AMBER Archive (2006)

Subject: RE: AMBER: Problem in Antechamber

From: Junmei Wang (jwang_at_encysive.com)
Date: Thu Jan 19 2006 - 17:02:39 CST

Hi, Sai,
Your molecule only contains heavy atoms and has open valence.
Antechamber can only handle molecules that have no open valences. Please
let me know if you still have problem after you add hydrogens
 
Regards
 
Junmei
 
 

==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang_at_encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================

        -----Original Message-----
        From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
On Behalf Of Sai Kumar Ramadugu
        Sent: Friday, January 13, 2006 12:02 AM
        To: amber_at_scripps.edu
        Subject: Re: AMBER: Problem in Antechamber
        
        
        Hi,
          I was giving option of -c bcc and was unable to create a
prepin file. But with what u mentioned in the mail, I was able to make a
prepin file.
         My pdb (of acridine and peptide only without DNA) is as
follows:
        
        HETATM 2910 C1 9AC 700 58.991 52.815 60.678
        HETATM 2911 C2 9AC 700 58.273 52.577 61.833
        HETATM 2912 C3 9AC 700 56.903 52.400 61.821
        HETATM 2913 C4 9AC 700 56.201 52.438 60.620
        HETATM 2914 C5 9AC 700 56.024 52.899 55.990
        HETATM 2915 C6 9AC 700 56.653 53.120 54.799
        HETATM 2916 C7 9AC 700 58.013 53.356 54.707
        HETATM 2917 C8 9AC 700 58.832 53.352 55.814
        HETATM 2918 C9 9AC 700 59.037 53.103 58.202
        HETATM 2919 N10 9AC 700 56.190 52.683 58.290
        HETATM 2920 C11 9AC 700 56.785 52.894 57.127
        HETATM 2921 C12 9AC 700 58.236 53.107 57.011
        HETATM 2922 C13 9AC 700 58.327 52.871 59.472
        HETATM 2923 C14 9AC 700 56.879 52.671 59.443
        HETATM 2924 C15 9AC 700 60.482 53.326 58.119
        HETATM 2925 O16 9AC 700 61.239 52.401 57.891
        ATOM 2926 N ARG 701 60.885 54.568 58.320
        ATOM 2927 CA ARG 701 62.319 54.946 58.385
        ATOM 2928 C ARG 701 63.020 54.255 59.556
        ATOM 2929 O ARG 701 62.395 53.986 60.595
        ATOM 2930 CB ARG 701 62.416 56.454 58.575
        ATOM 2931 CG ARG 701 61.610 57.260 57.581
        ATOM 2932 CD ARG 701 62.353 57.577 56.287
        TER
        
        Thanks and regards,
          Sai
        
        
        On 1/13/06, David A. Case <case_at_scripps.edu> wrote:

                On Tue, Jan 10, 2006, Sai Kumar Ramadugu wrote:
                
> I want to simulate a Drug-DNA complex. The complex
has
> acridine-peptide
(N-alpha(9-acridinoyl)-tetraarginine).
>
> Cannot successfully assign bond type for this
molecule, please :
> (1) double check the structure (the connectivity)
and/or
> (2) adjust atom valence penalty parameters in APS.DAT,
and/or
> (3) increase MAXVASTATE in define.h and recompile
bondtype.C
                
                Try giving the "-j 5" flags to the antechamber command.
                
>
> The prepin created doesnot have atom names.
                
                I have never seen this behavior. Can you post the pdb
input file you used;
                also the prepin file: what is put in place of the atom
names?
                
                ...dac

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