Re: [AMBER] antechamber dCTP

From: YZ Qin <yzqin.67.gmail.com>
Date: Fri, 8 Mar 2013 11:01:32 -0500

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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>



-- 
Yangzhong Qin
Physics, OSU




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Received on Fri Mar 08 2013 - 08:30:02 PST
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