Dear Francois,
Thank you for your reply!
I did try the F90. I can generate a dCTP2.mol file. Howerver, there are a
not of missing values in the frcmod file. Any suggstions on def
On Thursday, March 7, 2013, FyD wrote:
> 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!
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yangzhong Qin
Physics, OSU
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 07 2013 - 01:30:09 PST
