Hi All,
I am trying to study a protein-DNA-dCTP complex.
But I have a hard time on defining dCTP molecule, following the tutorial
http://ambermd.org/tutorials/basic/tutorial4b/.
I use the following command to generate dCTP.pdb, which looks fine to me.
reduce dCTP_orig3.pdb > dCTP.pdb
When I try to use
antechamber -i dCTP.pdb -fi pdb -o dCTP.mol2 -fo mol2 -c bcc -s 2 -nc -4
it reported error
Running: /usr/local/amber/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /usr/local/amber/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 240; net charge: -4
Running: /usr/local/amber/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/usr/local/amber/amber11/bin/sqm -O -i sqm.in -o
sqm.out" of bcc() in charge.c properly, exit
I look into the sqm.out, it says the following and stop at step 52
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1075E+07 DeltaE = 0.8621E+01 DeltaP = 0.5594E-01
QMMM: Smallest DeltaE = -0.1245E-03 DeltaP = 0.5847E-02 Step = 52
After I searched the archive, I change either 'tight-p-conv=0' or
'scfconv=1.0d-8', but it still report the same error but stopped at step
184.
I don't know the syntax for setting both values though.
I am stuck here for long time, please give me some help!
Thank you so much!
--
Yangzhong Qin
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Received on Wed Mar 06 2013 - 18:00:04 PST
