Dear Yangzhong Qin,
You could use R.E.D. or R.E.D. Server at q4md-forcefieldtools.org.
& you can find dCTP in R.E.DD.B.; please see:
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
More generally using sqm to directly optimize the geometry of dCTP is
unlikely to lead to a representative conformation in this case
(multiple negative charges).
regards, Francois
> 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!
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Received on Wed Mar 06 2013 - 23:00:02 PST
