Hi Bill,
Thank you for your suggestion!
I changed the pdb format from "C" to "CCC", and now it seems working. But
1200 atoms seems taking forever to finish.
I have the bond, angle, dihydral info for the molecule already. So is there
a way to input the bond information for antechamber (or other program) to
read to accelerate the prep file generation?
I notice that there is a "-a" option for additional file, with other
parameters "-fa" and "-ao".
I did following command:
*antechamber -i CNT.pdb -fi pdb -o CNT.prepin -fo prepi -a CNT_connect.pdb
-fa pdb -ao bond*
Where the CNT_connect.pdb looks like:
CONECT 18 17 19
CONECT 19 18 20 58
CONECT 20 19 21 61
CONECT 21 20 22
CONECT 22 21 23
CONECT 23 22 24 62
CONECT 24 23 25 65
Then it gave the error:
Error: cannot run "/home/CEAM/amber11/AmberTools-1.4/amber11/bin/prepgen -i
ANTECHAMBER_PREP.AC -f int -o 10106.prepin -rn "UNK" -rf molecule.res" in
wprep() of prep.c properly, exit
I guess that I used the wrong format for the "additional file",
Thanks and regards,
Yan
On Wed, Jul 14, 2010 at 11:27 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> All atoms within a residue must be named uniquely, so if you have
> 1200 atoms in your tube, you will need 1200 unique names. Since the
> pdb atom name format is limited, I suggest using letters rather than
> numbers (since there are [alphabet * 2 + 10] possibilities for each
> letter), e.g. instead of C1200, CZZ1.
>
> > ATOM 1 C UNK 1 6.779 0.000 -7.369 1.00 0.00
> > ATOM 2 C UNK 1 6.631 1.410 -7.369 1.00 0.00
> > ATOM 3 C UNK 1 6.447 2.095 -6.141 1.00 0.00
>
> Bill
>
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>
--
Yan Gao
Jacobs School of Engineering
University of California, San Diego
Tel: 858-952-2308
Email: Yan.Gao.2001.gmail.com
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Received on Wed Jul 14 2010 - 12:30:04 PDT
