This a sort of test I am doing and found something bizarre.
I have an ARG tri-peptide (NARG-ARG-CARG), but pretend you don't know this,
and I want to use antechamber to get its topology.
BTW, I use tleap to create the peptide and then sander to optimise it.
If I do:
------------------------------------------------------------------
antechamber -i agRRR.mol2 -fi mol2 -o agRRR_bcc_amber.mol2 -fo mol2 -c bcc
-nc 3 -m 1 -s 2 -df 2 -at amber -pf n
Running: /Users/alan/Programmes/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
---Judge bond type for Residue 1 with ID of 1 and Name of ARG ---
Info: Bond types are assigned for valence state 1 with penalty of 1
---Judge bond type for Residue 2 with ID of 2 and Name of ARG ---
Info: Bond types are assigned for valence state 15 with penalty of 1
---Judge bond type for Residue 3 with ID of 3 and Name of ARG ---
Info: Bond types are assigned for valence state 15 with penalty of 1
Running: /Users/alan/Programmes/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p amber
Total number of electrons: 262; net charge: 3
Running: /Users/alan/Programmes/amber11/bin/sqm -O -i sqm.in -o sqm.out
------------------------------------------------------------------
Then parmchk and tleap etc.
* It works. *
But if I want to use Gasteiger charges:
------------------------------------------------------------------
antechamber -i agRRR.mol2 -fi mol2 -o agRRR_gas_amber.mol2 -fo mol2 -c gas
-nc 3 -m 1 -s 2 -df 2 -at amber -pf n
Running: /Users/alan/Programmes/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
---Judge bond type for Residue 1 with ID of 1 and Name of ARG ---
Info: Bond types are assigned for valence state 1 with penalty of 1
---Judge bond type for Residue 2 with ID of 2 and Name of ARG ---
Info: Bond types are assigned for valence state 15 with penalty of 1
---Judge bond type for Residue 3 with ID of 3 and Name of ARG ---
Info: Bond types are assigned for valence state 15 with penalty of 1
Running: /Users/alan/Programmes/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0
-o ANTECHAMBER_AC.AC -p amber
Running: /Users/alan/Programmes/amber11/bin/atomtype -i ANTECHAMBER_GAS.AC-o
ANTECHAMBER_GAS_AT.AC -d
/Users/alan/Programmes/amber11/dat/antechamber/ATOMTYPE_GAS.DEF
The net charge of the molecule (3) does not equal to the total charge (3.00
) based on Gasteiger atom type, exit
------------------------------------------------------------------
This fails, since file agRRR_gas_amber.mol2 is not generated, so parmchk and
tleap will never work.
And if I use, for example babel, to get the Gasteiger charges in
my agRRR.mol2, and do:
antechamber -i agRRR.mol2 -fi mol2 -o agRRR_user_amber.mol2 -fo mol2 -c user
-nc 3 -m 1 -s 2 -df 2 -at amber -pf n
All works, with a tleap warning about the net charge generated by babel.
>From tleap log:
------------------------------------------------------------------
[snip]
ERROR: The unperturbed charge of the unit: 2.969400 is not integral.
WARNING: The unperturbed charge of the unit: 2.969400 is not zero.
-- ignoring the error and warning.
[snip]
------------------------------------------------------------------
But I get the prmtop and inpcrd files in the end.
So I am trying to understand why antechamber with gasteiger fails with an
incomprehensible error message:
"The net charge of the molecule (3) does not equal to the total charge (3.00
) based on Gasteiger atom type, exit"
Sounds like I have decimal rounds off problems here?
Many thanks,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Wed Aug 18 2010 - 02:00:03 PDT
