Hi Seçkin,
I can't comment on your methodology for producing the partial atomic charge. The resulting charges will depend upon what QM theory level was used. I can say that all of the amino acid residue within Amber were computed via resp - thus, to have a balanced charges one needs to use the resp weighting factors in their determination.
As your frcmod stand now, you have torsion parameters that are zero CT-C -N3-H and O-C-N3-H. This obviously will only effect the -NH3 rotational motion and conformations. However, how well it models this motion is unknown.
Concerning Wolf2Pack, as a general user the upload pdb button is deactivated. However, you have access to all of the existing molecules within the database; I also mentioned that you can tell me what internal coordinate is not present within the database and I will compute/upload it for you today. Based on the information given in your email, I will upload a protonated acetamide (i.e. acetamidium) that can be used to generate CT-C -N3-H and O-C-N3-H parameters. Any further questions/concerns about Wolf2Pack, please post them W2P's message board.
Cheers,
Karl
----- Original Message -----
From: "seçkin Boz" <bozseckin.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Thursday, May 9, 2013 1:45:46 PM
Subject: Re: [AMBER] ATTN: need revision
> I think the first thing to do is make sure you have the correct atom
> types assigned to your nonstandard residue. These are defined in the
> parameter files located in your $AMBERHOME/dat/leap/parm installation
> directory. You can also look at similar residues to see how they are
> defined there for equivalent atoms. Then run this through parmchk again to
> see if you have less (hopefully) of these lines.
>
I check the atom types and seems to me they are correct.
>
> Checking the frcmod output from parmchk and/or optimize the parameters
> is more difficult. The simplest way to "borrow" parameters from related
> terms, but this can be dangerous in my opinion. To properly do this will
> require performing some QM calculations for the internal coordinates that
> you are interested in and then comparing the resulting energy curves to the
> output of MM calculations. You might consider using wolf2pack (
> www.wolf2pack.com) to help guide you in doing this. If the existing
> molecular database does not contain the internal coordinates you need, then
> write a post on wolf2pack's message board and I will see what I can do for
> you. You also might consider using R.E.D. (
> http://q4md-forcefieldtools.org/RED/) to help create balanced partial
> atomic charges for your nonstandard residue.
>
> I perform QM calculation to obtain esp charges and add them into mol2 file
using script I wrote. This is my frcmod file and obviously N3 atom type is
problematic. Beacuse I add proton to that atom, and this is the only part
of my molecule which can be considered nonstandart. I look at wolf2pack but
loading pdb file button did not active. I've already perform MD using this
molecule. What are the possible consequences of leaving frcmod file as
this?
remark goes here
MASS
N 14.010 0.530 same as n
CT 12.010 0.878 same as c3
C 12.010 0.616 same as c
O 16.000 0.434 same as o
H 1.008 0.161 same as hn
H1 1.008 0.135 same as hc
HC 1.008 0.135 same as hc
N3 14.010 0.530 same as n4
BOND
N -CT 330.60 1.460 same as c3-n
N -H 410.20 1.009 same as hn-n
N -C 478.20 1.345 same as c -n
CT-C 328.30 1.508 same as c -c3
CT-H1 337.30 1.092 same as c3-hc
CT-CT 303.10 1.535 same as c3-c3
C -O 648.00 1.214 same as c -o
CT-HC 337.30 1.092 same as c3-hc
C -N3 255.50 1.546 same as c -n4
N3-H 369.00 1.033 same as hn-n4
ANGLE
N -CT-C 66.670 111.560 same as c -c3-n
N -CT-H1 49.780 109.500 same as hc-c3-n
N -CT-CT 65.850 112.130 same as c3-c3-n
N -C -CT 67.860 115.150 same as c3-c -n
N -C -O 75.830 122.030 same as n -c -o
CT-N -H 46.040 116.780 same as c3-n -hn
CT-N -C 63.920 121.350 same as c -n -c3
CT-C -O 68.030 123.110 same as c3-c -o
CT-CT-HC 46.370 110.050 same as c3-c3-hc
CT-CT-C 63.790 110.530 same as c -c3-c3
C -CT-H1 47.200 109.680 same as c -c3-hc
C -N -H 49.210 118.460 same as c -n -hn
H1-CT-CT 46.370 110.050 same as c3-c3-hc
CT-C -N3 64.610 112.260 same as c3-c -n4
HC-CT-HC 39.430 108.350 same as hc-c3-hc
HC-CT-C 47.200 109.680 same as c -c3-hc
C -N3-H 44.680 110.860 same as c -n4-hn
O -C -N3 69.580 118.830 same as n4-c -o
H -N3-H 40.520 108.110 same as hn-n4-hn
DIHE
N -CT-C -O 1 0.000 180.000 2.000 same as X -c
-c3-X
N -CT-C -N 1 1.700 180.000 -1.000 same as n -c3-c
-n
N -CT-C -N 1 2.000 180.000 2.000 same as n -c3-c
-n
N -CT-CT-HC 1 0.156 0.000 3.000 same as X
-c3-c3-X
N -CT-CT-C 1 0.156 0.000 3.000 same as X
-c3-c3-X
N -C -CT-H1 1 0.000 180.000 2.000 same as X -c
-c3-X
N -C -CT-CT 1 0.100 0.000 -4.000 same as c3-c3-c
-n
N -C -CT-CT 1 0.070 0.000 2.000 same as c3-c3-c
-n
CT-N -C -CT 1 2.500 180.000 2.000 same as X -c -n
-X
CT-N -C -O 1 2.500 180.000 2.000 same as X -c -n
-X
CT-C -N -H 1 2.500 180.000 2.000 same as X -c -n
-X
CT-CT-C -O 1 0.000 180.000 2.000 same as X -c
-c3-X
CT-CT-C -N3 1 0.000 180.000 2.000 same as X -c
-c3-X
C -CT-N -H 1 0.000 0.000 2.000 same as X -c3-n
-X
C -CT-N -C 1 0.850 180.000 -2.000 same as c -n
-c3-c
C -CT-N -C 1 0.800 0.000 1.000 same as c -n
-c3-c
C -CT-CT-HC 1 0.156 0.000 3.000 same as X
-c3-c3-X
C -CT-CT-C 1 0.156 0.000 3.000 same as X
-c3-c3-X
C -N -CT-H1 1 0.000 0.000 2.000 same as X -c3-n
-X
C -N -CT-CT 1 0.500 180.000 -4.000 same as c3-c3-n
-c
C -N -CT-CT 1 0.150 180.000 -3.000 same as c3-c3-n
-c
C -N -CT-CT 1 0.530 0.000 1.000 same as c3-c3-n
-c
O -C -CT-H1 1 0.800 0.000 -1.000 same as hc-c3-c
-o
O -C -CT-H1 1 0.080 180.000 3.000 same as hc-c3-c
-o
O -C -N -H 1 2.500 180.000 -2.000 same as hn-n -c
-o
O -C -N -H 1 2.000 0.000 1.000 same as hn-n -c
-o
H -N -CT-H1 1 0.000 0.000 2.000 same as X -c3-n
-X
H -N -CT-CT 1 0.000 0.000 2.000 same as X -c3-n
-X
H1-CT-CT-HC 1 0.150 0.000 3.000 same as
hc-c3-c3-hc
H1-CT-CT-C 1 0.156 0.000 3.000 same as X
-c3-c3-X
CT-C -N3-H 1 0.000 0.000 0.000 ATTN, need
revision
HC-CT-C -O 1 0.800 0.000 -1.000 same as hc-c3-c
-o
HC-CT-C -O 1 0.080 180.000 3.000 same as hc-c3-c
-o
HC-CT-C -N3 1 0.000 180.000 2.000 same as X -c
-c3-X
O -C -N3-H 1 0.000 0.000 0.000 ATTN, need
revision
IMPROPER
C -CT-N -H 1.1 180.0 2.0 Using default
value
CT-N -C -O 1.1 180.0 2.0 Using default
value
CT-N3-C -O 1.1 180.0 2.0 Using default
value
NONBON
N 1.8240 0.1700 same as n
CT 1.9080 0.1094 same as c3
C 1.9080 0.0860 same as c
O 1.6612 0.2100 same as o
H 0.6000 0.0157 same as hn
H1 1.4870 0.0157 same as hc
HC 1.4870 0.0157 same as hc
N3 1.8240 0.1700 same as n4
Thank you for your reply
Sincerely
seckin
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Received on Mon May 13 2013 - 00:30:02 PDT
