Any suggestions on defining those bond and diahedral parameters? Or I can
randomly start with some guess?
On Thursday, March 7, 2013, YZ Qin wrote:
> 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!
>>
>>
>>
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>>
>
>
> --
> Yangzhong Qin
>
> Physics, OSU
>
--
Yangzhong Qin
Physics, OSU
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Received on Thu Mar 07 2013 - 01:30:12 PST
