AMBER Archive (2006)

Subject: Re: AMBER: Problem in Antechamber

From: Sai Kumar Ramadugu (compchem123_at_gmail.com)
Date: Fri Jan 13 2006 - 00:01:46 CST

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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