Dear Users
I wanted to follow up on my previous query regarding the Error in
Antechamber.
Below is my original question for reference:
I want to run Antechamber for an organic molecule consisting of 280 atoms,
which was optimized and assigned charges using the following parameters:
Initially, the molecule was optimized using:
*1*.%NProcShared=16
%mem=16GB
%chk=opt.chk
# opt b3lyp/6-31g geom=connectivity
Using output from *1, *I ran:
*2*.%NProcShared=16
%mem=16GB
%chk=opt2.chk
#p b3lyp/6-31+g(d,p) pop=MK iop(6/33=2, 6/42=6) nosymm
scf(xqc,maxcycle=9999)
Then using output log file of *2,* I ran:
*3*.%nprocshared=16
%mem=16GB
%chk=est_grid.chk
#p b3lyp/6-31+g(d,p) nosymm iop(6/33=2,6/42=6) scf=(xqc,maxcycle=9999)
pop(chelpg,regular)
Finally, I tried to run Antechamber using the final output log file with
the following command:
*antechamber -i est_grid.log -fi gout -o est_grid.mol2 -fo mol2 -c resp -nc
0 -m 1 -rn MOL*
However, I encountered the following warning messages:
Warning: atom type of C41 (cc) and C42 (cd) may be wrong.
Warning: atom type of C85 (cc) and C86 (cd) may be wrong.
Warning: atom type of C151 (cc) and C152 (cd) may be wrong.
Additionally, at the end of the process, I received this error:
/home/s/miniconda3/envs/AmberTools23/bin/wrapped_progs/antechamber: Fatal
Error!
Cannot properly run "/home/s/miniconda3/envs/AmberTools23/bin/respgen -i
ANTECHAMBER_RESP.AC <
http://antechamber_resp.ac/> -o ANTECHAMBER_RESP1.IN
<
http://antechamber_resp1.in/> -f resp1 -e 1".
Could anyone help me resolve this issue?
I would really appreciate any insights or suggestions.
Thank you for your time.
On Thu, Mar 27, 2025 at 11:21 AM Devid Sahu <ds890.snu.edu.in> wrote:
> Dear Users
>
> I want to run Antechamber for an organic molecule consisting of 280 atoms,
> which was optimized and assigned charges using the following parameters:
>
> Initially, the molecule was optimized using:
> *1*.%NProcShared=16
> %mem=16GB
> %chk=opt.chk
> # opt b3lyp/6-31g geom=connectivity
>
> Using output from *1, *I ran:
> *2*.%NProcShared=16
> %mem=16GB
> %chk=opt2.chk
> #p b3lyp/6-31+g(d,p) pop=MK iop(6/33=2, 6/42=6) nosymm
> scf(xqc,maxcycle=9999)
>
> Then using output log file of *2,* I ran:
> *3*.%nprocshared=16
> %mem=16GB
> %chk=est_grid.chk
> #p b3lyp/6-31+g(d,p) nosymm iop(6/33=2,6/42=6) scf=(xqc,maxcycle=9999)
> pop(chelpg,regular)
>
> Finally, I tried to run Antechamber using the final output log file with
> the following command:
> *antechamber -i est_grid.log -fi gout -o est_grid.mol2 -fo mol2 -c resp
> -nc 0 -m 1 -rn MOL*
>
> However, I encountered the following warning messages:
> Warning: atom type of C41 (cc) and C42 (cd) may be wrong.
> Warning: atom type of C85 (cc) and C86 (cd) may be wrong.
> Warning: atom type of C151 (cc) and C152 (cd) may be wrong.
>
> Additionally, at the end of the process, I received this error:
> /home/s/miniconda3/envs/AmberTools23/bin/wrapped_progs/antechamber: Fatal
> Error!
> Cannot properly run "/home/s/miniconda3/envs/AmberTools23/bin/respgen -i
> ANTECHAMBER_RESP.AC -o ANTECHAMBER_RESP1.IN -f resp1 -e 1".
>
> Could anyone help me resolve this issue? Any suggestions would be highly
> appreciated.
>
> Thanks!!
>
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Received on Fri Mar 28 2025 - 03:00:02 PDT
