Dear Amber Prof Dac and Anselim
Thank you
It gives error of open valence
antechamber -i floB.mol2 -fi mol2 -o floB.com -fo gcrt
Welcome to antechamber: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: The number of bonds (2) for atom (ID: 32, Name: O4) does not match
the connectivity (1) for atom type (O.2) defined in
CORR_NAME_TYPE.DAT.
Warning: The number of bonds (3) for atom (ID: 34, Name: C17) does not match
the connectivity (4) for atom type (C.3) defined in
CORR_NAME_TYPE.DAT.
But, you may safely ignore the warnings if your molecule
uses atom names or element names as atom types.
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
/home/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (3) for atom (ID: 34, Name: C17).
Possible open valence.
*Dear Anselim*
should I mention charge in same command? can you please suggest me?
Is it a good choice to write gaussian input file in Avogadros and then do
geometry optimization?
Also could you please suggest me how to make a resp.in file from
floBF_esp.dat as mentioned in same tutorial
http://ambermd.org/tutorials/advanced/tutorial1/section1.htm after doing cat
floB_esp.dat floF_esp.dat > floBF_esp.dat
should I convert floBF_esp.dat file in to .ac file for respgen program to
make a resp input file? as mentioend below:-
respgen -i sustiva.ac -o sustiva.respin1 -f resp1
Need suggesstions
thank you
Sadaf
On Thu, Jul 18, 2019 at 2:26 PM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Am 18.07.2019 um 14:22 schrieb David A Case:
> > On Wed, Jul 17, 2019, Sadaf Rani wrote:
> >
> >> antechamber -i floB.mol2 -fi pdb -o floB.com -fo gcrt
> >
> > First, use "-fi mol2" since your input file is mol2, not pdb.
> >
> > Second, consider the messages from acdoctor, but if you are convinced
> > your structure is correct, add "-dr no" to turn off the acdoctor checks.
> >
> > With those changes, I get a floB.com file that looks OK (didn't actually
> > run it with Gaussian, however.)
>
> A short additional note:
>
> However, when looking at the structure I noticed that the total charge
> of the system is most probably not 0, and thus should be specified
> explicitely in the antechamber invocation, in order to create a Gaussian
> input for the correct electronic configuration.
>
> Regards,
>
> Anselm
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 18 2019 - 14:00:01 PDT
