AMBER Archive (2003)

Subject: Re: AMBER pdb help - lost atoms - Part 2

From: kxg2248_at_njit.edu
Date: Thu Apr 03 2003 - 11:50:29 CST

I was attempting to convert my pdb to AMBER topology and coordinate files,
using the commands:
antechamber -i GC.pdb -fi pdb -o GC.prepin -fo prepi -c gas
parmchk -i GC.prepin -f prepi -o GC_frcmod

After the antechamber command, the prepi and NEWPDB.PDB files have only 15
of 26 atoms that were in the original input file, but the
ANTECHAMBER_GAS.AC and ANTECHAMBER_GAS_AT.AC files do have all 26
atoms. The pdb file basically is a G-C pair with no sugars or phosphates.

I tried to use tleap to create a unit containing the pdb, but I get so many
additional atoms using the standard residue names that the results are
useless to me. I'm thinking I need to create my own templates for each
residue, and use leap. Once again, thanks for your help - I'll start on
the custom templates and that should solve my problem with lost atoms.

Thanks,
K. Gilbert
NJIT

COMPND GC
ATOM 1 C1 DCN3 1 2.1472 -4.424 2.4696
ATOM 2 N1 DCN3 1 -2.157 -2.191 -0.174
ATOM 3 H1 DCN3 1 -2.098 -1.226 -0.465
ATOM 4 H2 DCN3 1 -2.992 -2.728 -0.366
ATOM 5 C4 DCN3 1 -1.142 -2.754 0.4626
ATOM 6 N3 DCN3 1 -0.054 -2.012 0.7042
ATOM 7 C2 DCN3 1 1.0164 -2.539 1.3482
ATOM 8 O2 DCN3 1 2.0354 -1.878 1.5860
ATOM 9 N2 DCN3 1 0.9622 -3.867 1.7629
ATOM 10 C6 DCN3 1 -0.137 -4.626 1.5243
ATOM 11 C5 DCN3 1 -1.224 -4.118 0.8821
TER
ATOM 12 C7 DGN3 2 0.9446 5.5853 -1.569
ATOM 13 N4 DGN3 2 2.2610 0.9093 0.4863
ATOM 14 H3 DGN3 2 2.1932 -0.040 0.7906
ATOM 15 H4 DGN3 2 3.1036 1.4041 0.6068
ATOM 16 O6 DGN3 2 -2.085 0.4135 -0.876
ATOM 17 C8 DGN3 2 -1.130 1.1864 -0.800
ATOM 18 C9 DGN3 2 -1.035 2.5301 -1.228
ATOM 19 N5 DGN3 2 -1.983 3.3480 -1.848
ATOM 20 C10 DGN3 2 -1.359 4.4859 -2.012
ATOM 21 N6 DGN3 2 -0.059 4.4880 -1.551
ATOM 22 C11 DGN3 2 0.1464 3.2247 -1.043
ATOM 23 N7 DGN3 2 1.3009 2.7773 -0.482
ATOM 24 C12 DGN3 2 1.2138 1.5101 -0.087
ATOM 25 N8 DGN3 2 0.0731 0.7456 -0.222
ATOM 26 H5 DGN3 2 0.0628 -0.199 0.1041
TER

>On Thu, Apr 03, 2003, kxg2248_at_njit.edu wrote:
>
>
> > Thanks for the responses on my first post. I've tried even more
> methods to
> > get my pdb file to be completely read in, but even starting with nukit,
> > then nucgen, then leap or antechamber doesn't seem to work.
>
>
>Sorry, my memory of your problem is not what you think it is. Saying
>"leap or antechamber doesn't seem to work" doesn't help enough. Exactly
>what commands did you give, and what was the result?
>
>
> > And leap
> > insists on adding the sugar and phosphate to each base, and I am not using
> > them in my study.
>
>
>If you want to use the standard libraries for nucleic acids, then LEaP
>will indeed add atoms that it needs to get that standard moiety. If you
>want to model something that is not in the standard library, you need to
>make your own templates. You can do this by editing an existing template
>(change the residue name to avoid confusion with the standard names), or
>use antechamber to build the template for you.
>
>
>.good luck...dac