Dear Yangzhong Qin,
Here you have to modify the FF lib of dCTP by hand so that:
- you have a single residue (and obviously two atoms in a given
residue cannot share the same name: modify the atom names of the
phosphate!)
- then modify your PDB file (residue & atom names) accordingly.
the new version of R.E.D. will handle this problem, and the user will
have the possibility to choose between a FF lib composed of several
residues or force the generation of a single residue (and atom
renaming).
more generally loading a FF lib composed of several residues is ok for
studying this molecule by itself, but not docked in a macrostructure
co (as in your case).
regards, Francois
Quoting YZ Qin <yzqin.67.gmail.com>:
> Hi Francois,
>
> Following your suggestions, I have got the dCTP2 and successfully load it
> into leap. Thank you so much!
>
> However, some other problems came up. I should've told you my project in
> more detail before. If this wastes too much time, I am really sorry for
> that.
>
> Here is what I am doing:
>
> I have a protein-DNA-dCTP2 complex along with its pdb file downloaded from
> the protein data bank.
> When I load the pdb file into leap, I have a problem with recognizing the
> CTP residue.
> Now I have the dCTP2 file in the library, but leap still couldn't recognize
> this CTP.
> I know I need to modify the pdb file so that it can match dCTP2 before
> loading to leap.
> But dCTP2 consists of four residues (P2M, P1, P1, C5), and I think leap
> requires that one residue should have all the atoms named uniquely. My
> current understanding is that leap will not recognize my CTP in pdb file
> due to different formatting.
>
> I searched the archive and found that people had similar problems long time
> before, unfortunately I didn't find a good solution to that.
>
> I was wondering is there a good solution for this kind of problem now ? or
> there is a way to go around it.
>
>
> Here is the file I am using:
> Ternary3.pdb (I did some modification and tried to match the dCTP2, but
> this didn't work or something was wrong )
> dCTP2.off
>
>
> Really sorry for bothering you so long!
>
> Have a nice day!
>
>
>
>
>
>
> On Thu, Mar 7, 2013 at 3:45 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> 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 Fri Mar 08 2013 - 23:30:03 PST
