Hi,
I responded to this yesterday, maybe you missed it. I'll paste my
response below just in case:
It looks like you are trying to parameterize an entire protein using
antechamber, which is the wrong approach. Antechamber is designed for
developing parameters for small ligands, cofactors, building blocks of
larger molecules (e.g. amino acids), etc. Force fields with parameters
for standard amino acids already exist; the correct approach is to use
the 'LEaP' program to load one of these force fields, load your
structure, then write out a topology and restart file which can be
used for MD. I highly recommend you run through a few of the Amber
tutorials (
http://ambermd.org/tutorials/), especially B1, as well as
read chapters 2 and 4 of the AmberTools 13 manual.
-Dan
On Wed, Oct 2, 2013 at 6:36 AM, Tanmoy Paul <tanmoy635.gmail.com> wrote:
> Dear Amber users,
> I am trying to fit resp charges to HCA2(
> pdb code 2CBA) using antechamber. I have generated the Final.esp file
> from gaussian 09. Now when I am
> giving the following command
>
> antechamber -i HCA_final.esp -fi gesp -o HCA.prepin -fo prepi -c resp
> -s 2 -rn HCA
> -at amber -nc 2
>
> the output looks like.............
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
>
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> Info: the actual number of rings (810) exceeds the defaut ring size
> (500), reallocate memory automatically
> For atom[725]:O137, the best APS is not zero, bonds involved by this
> atom are frozen
>
> For atom[746]:O139, the best APS is not zero, bonds involved by this
> atom are frozen
>
> For atom[929]:O175, the best APS is not zero, bonds involved by this
> atom are frozen
>
> For atom[2060]:Zn1, the best APS is not zero, bonds involved by this
> atom are frozen
>
> ---Judge bond type for Residue 1 with ID of 1 and Name of MOL ---
> Error: cannot run "/usr/local/AMBER12/amber12/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
> and another interesting fact is , in the programme generated
> "ANTECHAMBER_BOND_TYPE.AC0 " file the whole bond type column
> comprises
> only zero. It may be the reason behind the programme termination. Now
> I don't know
> how to fix this. Please help me.
>
> Tanmoy Paul
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Oct 02 2013 - 09:00:04 PDT
