AMBER Archive (2006)

Subject: Re: AMBER: Problem in Antechamber

From: Sai Kumar Ramadugu (compchem123_at_gmail.com)
Date: Thu Jan 26 2006 - 22:46:42 CST

Hi Sir,
   When I used antechamber with -j 5, I could get the prepin file with out
any problesm.
Thanks for the help from Prof. DA Case and u.
Regards,
  Sai

On 1/20/06, Junmei Wang <jwang_at_encysive.com> wrote:
>
> 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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