Dear Amber users
I want to make gaussian input file of pdb structure from the following
command:-
antechamber -i floB.pdb -fi pdb -o floB.com -fo gcrt
but it gives the following message:-
Welcome to antechamber: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Warning: Close ( 1.09) nonbonded atoms (ID: 1, Name: C) and (ID: 2, Name:
H).
Warning: Close ( 1.10) nonbonded atoms (ID: 1, Name: C) and (ID: 3, Name:
H1).
Warning: Close ( 1.10) nonbonded atoms (ID: 1, Name: C) and (ID: 4, Name:
H2).
Warning: Close ( 1.44) nonbonded atoms (ID: 1, Name: C) and (ID: 5, Name:
N).
Warning: Close ( 1.01) nonbonded atoms (ID: 5, Name: N) and (ID: 6, Name:
H3).
Warning: Close ( 1.38) nonbonded atoms (ID: 5, Name: N) and (ID: 7, Name:
C1).
Warning: Close ( 1.23) nonbonded atoms (ID: 7, Name: C1) and (ID: 8, Name:
O).
Warning: Close ( 1.49) nonbonded atoms (ID: 7, Name: C1) and (ID: 9, Name:
C2).
Warning: Close ( 1.40) nonbonded atoms (ID: 9, Name: C2) and (ID: 10, Name:
C3).
Warning: Close ( 1.40) nonbonded atoms (ID: 9, Name: C2) and (ID: 19, Name:
C8).
Warning: Close ( 1.09) nonbonded atoms (ID: 10, Name: C3) and (ID: 11,
Name: H4).
Warning: Close ( 1.40) nonbonded atoms (ID: 10, Name: C3) and (ID: 12,
Name: C4).
Warning: Close ( 1.56) nonbonded atoms (ID: 12, Name: C4) and (ID: 13,
Name: C5).
Warning: Close ( 1.41) nonbonded atoms (ID: 12, Name: C4) and (ID: 16,
Name: C6).
Warning: Close ( 1.26) nonbonded atoms (ID: 13, Name: C5) and (ID: 14,
Name: O1).
Warning: Close ( 1.25) nonbonded atoms (ID: 13, Name: C5) and (ID: 15,
Name: O2).
Warning: Close ( 1.41) nonbonded atoms (ID: 16, Name: C6) and (ID: 17,
Name: C7).
Warning: Close ( 1.50) nonbonded atoms (ID: 16, Name: C6) and (ID: 21,
Name: C9).
Warning: Close ( 1.09) nonbonded atoms (ID: 17, Name: C7) and (ID: 18,
Name: H5).
Warning: Close ( 1.39) nonbonded atoms (ID: 17, Name: C7) and (ID: 19,
Name: C8).
Warning: Close ( 1.09) nonbonded atoms (ID: 19, Name: C8) and (ID: 20,
Name: H6).
Warning: Close ( 1.41) nonbonded atoms (ID: 21, Name: C9) and (ID: 22,
Name: C10).
Warning: Close ( 1.41) nonbonded atoms (ID: 21, Name: C9) and (ID: 34,
Name: C17).
Warning: Close ( 1.43) nonbonded atoms (ID: 22, Name: C10) and (ID: 23,
Name: C11).
Warning: Close ( 1.43) nonbonded atoms (ID: 22, Name: C10) and (ID: 31,
Name: C15).
Warning: Close ( 1.09) nonbonded atoms (ID: 23, Name: C11) and (ID: 24,
Name: H7).
Warning: Close ( 1.37) nonbonded atoms (ID: 23, Name: C11) and (ID: 25,
Name: C12).
Warning: Close ( 1.09) nonbonded atoms (ID: 25, Name: C12) and (ID: 26,
Name: H8).
Warning: Close ( 1.46) nonbonded atoms (ID: 25, Name: C12) and (ID: 27,
Name: C13).
Warning: Close ( 1.26) nonbonded atoms (ID: 27, Name: C13) and (ID: 28,
Name: O3).
Warning: Close ( 1.45) nonbonded atoms (ID: 27, Name: C13) and (ID: 29,
Name: C14).
Warning: Close ( 1.09) nonbonded atoms (ID: 29, Name: C14) and (ID: 30,
Name: H9).
Warning: Close ( 1.37) nonbonded atoms (ID: 29, Name: C14) and (ID: 31,
Name: C15).
Warning: Close ( 1.37) nonbonded atoms (ID: 31, Name: C15) and (ID: 32,
Name: O4).
Warning: Close ( 1.37) nonbonded atoms (ID: 32, Name: O4) and (ID: 33,
Name: C16).
Warning: Close ( 1.43) nonbonded atoms (ID: 33, Name: C16) and (ID: 34,
Name: C17).
Warning: Close ( 1.37) nonbonded atoms (ID: 33, Name: C16) and (ID: 41,
Name: C21).
Warning: Close ( 1.43) nonbonded atoms (ID: 34, Name: C17) and (ID: 35,
Name: C18).
Warning: Close ( 1.09) nonbonded atoms (ID: 35, Name: C18) and (ID: 36,
Name: H10).
Warning: Close ( 1.37) nonbonded atoms (ID: 35, Name: C18) and (ID: 37,
Name: C19).
Warning: Close ( 1.09) nonbonded atoms (ID: 37, Name: C19) and (ID: 38,
Name: H11).
Warning: Close ( 1.46) nonbonded atoms (ID: 37, Name: C19) and (ID: 39,
Name: C20).
Warning: Close ( 1.26) nonbonded atoms (ID: 39, Name: C20) and (ID: 40,
Name: O5).
Warning: Close ( 1.45) nonbonded atoms (ID: 39, Name: C20) and (ID: 41,
Name: C21).
Warning: Close ( 1.09) nonbonded atoms (ID: 41, Name: C21) and (ID: 42,
Name: H12).
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
/home/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
This molecule may have more than one unit.
antechamber can only handle one unit. If the input is a single unit
then the connectivity is wrong and the geometry may be bad.
Please convert your molecule to a mol2 file via:
antechamber -j 5 -at sybyl -dr no
And then check your molecule with a visualization program;
manually add missing bonds or delete unwanted bonds as appropriate.
then I converted pdb file in to mol2 using Avgadros and used this command:-
antechamber -i floB.mol2 -fi pdb -o floB.com -fo gcrt
It gives following message:-
Welcome to antechamber: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: This molecule has no hydrogens nor halogens.
It is quite possible that there are unfilled valences.
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
But if I open floB.com file there are no any coordinates and is as follows:-
--Link1--
%chk=molecule
#HF/<F2>^C SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
remark line goes here
0 1
floB.com (END)
Could you please suggest me what would be the error and how to fix it?
mol2 and com file (as txt file) is attached please.
I am following following tutorial and using the pdb as mentioend in
tutorial:-
http://ambermd.org/tutorials/advanced/tutorial1/section1.htm
Sadaf
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- application/octet-stream attachment: floB.mol2
Received on Wed Jul 17 2019 - 12:30:02 PDT
