Yangzhong Qin,
the frcmod file is already provided in F-90; no need to use parmchk
please read the script1.ff: you will see that script3.ff (i.e. a
frcmod file) is already loaded...
regards, Francois
Quoting YZ Qin <yzqin.67.gmail.com>:
> Thank you Francois, your suggestion is really helpful!
>
> After running scipt1.ff, I get a dCTP2.mol2 file. Then I run the following
> command
>
> parmchk -i dCTP2.mol2 -f mol2 -o dCTP2.frcmod
>
> and get the dCTP2.frcmod as the following:
>
>
> **********************
>
> remark goes here
> MASS
> O 16.000 0.434 same as o
> P 30.970 1.538 same as p4
> H 1.008 0.161 same as hn
> C 12.010 0.616 same as c
> N 14.010 0.530 same as n
>
> BOND
> O -P 456.40 1.503 same as o -p4
> O -C 648.00 1.214 same as c -o
> O -H 0.00 0.000 ATTN, need revision
> C -H 0.00 0.000 ATTN, need revision
> C -C 290.10 1.550 same as c -c
> C -N 478.20 1.345 same as c -n
> N -H 410.20 1.009 same as hn-n
>
> ANGLE
> O -P -O 72.010 117.220 same as o -p4-o
> P -O -P 0.000 0.000 ATTN, need revision
> O -C -C 67.160 120.990 same as c -c -o
> O -C -H 0.000 0.000 ATTN, need revision
> P -O -C 0.000 0.000 ATTN, need revision
> H -O -C 0.000 0.000 ATTN, need revision
> C -C -H 0.000 0.000 ATTN, need revision
> C -C -C 62.300 111.680 same as c -c -c
> C -O -C 0.000 0.000 ATTN, need revision
> C -N -C 65.330 127.140 same as c -n -c
> H -C -N 0.000 0.000 ATTN, need revision
> C -C -N 67.530 112.140 same as c -c -n
> H -C -H 0.000 0.000 ATTN, need revision
> O -C -N 75.830 122.030 same as n -c -o
> N -C -N 74.800 113.380 same as n -c -n
> H -N -H 39.730 117.850 same as hn-n -hn
> H -N -C 48.395 122.495 Calculated with empirical approach
>
> DIHE
> O -P -O -P 1 0.000 0.000 0.000 ATTN, need
> revision
> O -P -O -C 1 0.000 0.000 0.000 ATTN, need
> revision
> O -C -C -C 1 0.300 180.000 2.000 same as X -c -c
> -X
> O -C -C -H 1 0.300 180.000 2.000 same as X -c -c
> -X
> O -C -C -O 1 0.300 180.000 2.000 same as X -c -c
> -X
> P -O -C -C 1 0.000 0.000 0.000 ATTN, need
> revision
> P -O -C -H 1 0.000 0.000 0.000 ATTN, need
> revision
> H -O -C -C 1 0.000 0.000 0.000 ATTN, need
> revision
> H -O -C -H 1 0.000 0.000 0.000 ATTN, need
> revision
> C -C -C -H 1 0.300 180.000 2.000 same as X -c -c
> -X
> C -C -C -C 1 0.300 180.000 2.000 same as X -c -c
> -X
> C -O -C -C 1 0.000 0.000 0.000 ATTN, need
> revision
> C -O -C -H 1 0.000 0.000 0.000 ATTN, need
> revision
> C -N -C -N 1 2.500 180.000 2.000 same as X -c -n
> -X
> C -N -C -O 1 2.500 180.000 2.000 same as X -c -n
> -X
> C -N -C -H 1 2.500 180.000 2.000 same as X -c -n
> -X
> C -N -C -C 1 2.500 180.000 2.000 same as X -c -n
> -X
> H -C -C -H 1 0.300 180.000 2.000 same as X -c -c
> -X
> H -C -C -N 1 0.300 180.000 2.000 same as X -c -c
> -X
> C -C -C -N 1 0.300 180.000 2.000 same as X -c -c
> -X
> C -O -C -N 1 0.000 0.000 0.000 ATTN, need
> revision
> H -N -C -N 1 2.500 180.000 2.000 same as X -c -n
> -X
> H -N -C -C 1 2.500 180.000 2.000 same as X -c -n
> -X
>
> IMPROPER
> C -H -C -O 1.1 180.0 2.0 Using default
> value
> C -H -C -H 1.1 180.0 2.0 Using default
> value
> C -C -C -H 1.1 180.0 2.0 Using default
> value
> H -H -C -O 1.1 180.0 2.0 Using default
> value
> C -H -N -H 1.1 180.0 2.0 Using default
> value
> C -N -C -N 1.1 180.0 2.0 Using default
> value
> N -N -C -O 1.1 180.0 2.0 Using default
> value
> C -C -N -C 1.1 180.0 2.0 Using default
> value
> C -H -C -N 1.1 180.0 2.0 Using default
> value
>
> NONBON
> O 1.6612 0.2100 same as o
> P 2.1000 0.2000 same as p4
> H 0.6000 0.0157 same as hn
> C 1.9080 0.0860 same as c
> N 1.8240 0.1700 same as n
>
> *******************************
>
> By "missing values", I mean those values set to "0" and marked with ATTN.
>
> Did I miss something?
>
>
> Thank you so much!
>
>
>
>
> On Thu, Mar 7, 2013 at 5:55 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Yangzhong Qin,
>>
>> > 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
>>
>> there is a frcmod file:
>> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script3.ff
>>
>> if you to use the script1.ff
>> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
>>
>> you need to apply different commands before to use this script1.ff:
>> perl -p -i.old -e 's/\#\#\!\# //g' script1.ff
>> grep -v "to be replaced by the correct tripos" script1.ff >
>> script1-new.ff
>>
>> Does it help?
>>
>> by missing values - what do you mean?
>> could you provide the error message generated by LEaP?
>>
>> regards, Francois
>>
>>
>> > 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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Received on Thu Mar 07 2013 - 13:00:03 PST
