Dear Francois,
I run again the Ante_R.E.D. 1.4 and also Ante_R.E.D. 2.0 . R.E.D,
but i am still getting errors when I am loading the mol2 file to the xleap ...
1 N 0.605380 0.819932 -0.576060 N 1 PYA -0.7057 ****
2 H 0.174989 0.824523 -1.472280 H 1 PYA 0.3686 ****
3 CA 0.730348 -0.452452 0.117596 CT 1 PYA 0.1959 ****
4 HA 0.639473 -0.241084 1.173722 H1 1 PYA 0.0965 ****
5 CB -0.369688 -1.423667 -0.320567 CT 1 PYA -0.0206 ****
6 HB2 -0.233967 -1.663736 -1.367613 HC 1 PYA 0.0018 ****
7 HB3 -0.227914 -2.352854 0.219720 HC 1 PYA 0.0018 ****
8 CG -1.766459 -0.896904 -0.076042 CA 1 PYA 0.1963 ****
9 CD1 -2.623650 -0.605483 -1.126238 CA 1 PYA -0.3512 ****
10 HD1 -2.321269 -0.760458 -2.146784 HA 1 PYA 0.1613 ****
11 CD2 -2.253978 -0.688025 1.209409 CA 1 PYA -0.3512 ****
12 HD2 -1.651676 -0.902180 2.074037 HA 1 PYA 0.1613 ****
13 CE1 -3.893742 -0.122764 -0.850677 CB 1 PYA 0.2935 ****
14 HE1 -4.569416 0.106050 -1.656600 H4 1 PYA 0.0700 ****
15 CE2 -3.537068 -0.201541 1.372658 CB 1 PYA 0.2935 ****
16 HE2 -3.928313 -0.034089 2.360846 H4 1 PYA 0.0700 ****
17 NZ -4.350531 0.082106 0.368715 NC 1 PYA -0.5622 ****
18 C 2.117472 -1.058764 -0.143516 C 1 PYA 0.1611 ****
19 O 2.279254 -1.956249 -0.927864 O 1 PYA -0.1216 ****
> check x
Checking 'x'....
Checking parameters for unit 'x'.
Checking for bond parameters.
Could not find bond parameter for: CB - H4
Could not find bond parameter for: CB - H4
Checking for angle parameters.
Could not find angle parameter: CA - CB - H4
Could not find angle parameter: CA - CB - NC
Could not find angle parameter: CA - CB - H4
Could not find angle parameter: CA - CB - NC
Could not find angle parameter: CB - NC - CB
Could not find angle parameter: H4 - CB - NC
Could not find angle parameter: H4 - CB - NC
There are missing parameters.
the atom types seem to be still wrong ...
/Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Dienstag, 6. Dezember 2011 17:37
An: AMBER Mailing List
Betreff: Re: [AMBER] atom types for pyridine II...
Dear Urszula,
Sorry an error in my previous email: CB vs CM...
> I will change the atom names for the next time, but for the
> pyridinie I have already necessary files and dont want to run
> gaussian,
ok, I understand. However, does it make sense to name H11 the name of
the hydrogen atom, which is connected to C12 and H12 that is connected
to C11 ;-) ?
If you modify the names in the P2N file and you use the Refit-mode of
III.x, only charge fitting & FF library building are performed.
I read the parm99.dat file, and edit the PHE, TYR, HIS, DC and DT
residues to get examples of FF atom types:
1 N 0.605380 0.819932 -0.576060 N 1 PYA
-0.4348
2 H 0.174989 0.824523 -1.472280 H 1 PYA
0.2971
3 CA 0.730348 -0.452452 0.117596 CT 1 PYA
0.0305
4 HA 0.639473 -0.241084 1.173722 H1 1 PYA
0.0603
5 CB -0.369688 -1.423667 -0.320567 CT 1 PYA
-0.0171
6 HB2 -0.233967 -1.663736 -1.367613 HC 1 PYA
0.0573
7 HB3 -0.227914 -2.352854 0.219720 HC 1 PYA
0.0573
8 CG -1.766459 -0.896904 -0.076042 CA 1 PYA
0.1171
9 CD1 -2.623650 -0.605483 -1.126238 CA 1 PYA
-0.3646
10 HD1 -2.321269 -0.760458 -2.146784 HA 1 PYA
0.1558
11 CD2 -2.253978 -0.688025 1.209409 CA 1 PYA
-0.2597
12 HD2 -1.651676 -0.902180 2.074037 HA 1 PYA
0.1277
13 CE1 -3.893742 -0.122764 -0.850677 CM 1 PYA
0.3138
14 HE1 -4.569416 0.106050 -1.656600 H4 1 PYA
0.0636
15 CE2 -3.537068 -0.201541 1.372658 CM 1 PYA
0.2798
16 HE2 -3.928313 -0.034089 2.360846 H4 1 PYA
0.0689
17 NZ -4.350531 0.082106 0.368715 NC 1 PYA
-0.5709
18 C 2.117472 -1.058764 -0.143516 C 1 PYA
0.5924
19 O 2.279254 -1.956249 -0.927864 O 1 PYA
-0.5743
Moreover:
- my understanding is that the charges of the CD1 and CD2 atoms should
be equivalent, and they are not...
- same idea for HD1 and HD2, CE1 and CE2 as well as HE1 and HE2
Did you use Ante_R.E.D. 1.4 to generate the P2N file? if so, please
use Ante_R.E.D. 2.0 . R.E.D. Server;
see
http://q4md-forcefieldtools.org/REDS/news.php
http://q4md-forcefieldtools.org/REDS/popup/popanteredtopequiv.php
regards, Francois
> I have changed the atom types for my molecule as you suggested but
> there is still a problem ...
>
> check x
> Checking 'x'....
> Checking parameters for unit 'x'.
> Checking for bond parameters.
> Could not find bond parameter for: CB - H4
> Could not find bond parameter for: CB - H4
> Checking for angle parameters.
> Could not find angle parameter: CA - CB - H4
> Could not find angle parameter: CA - CB - NC
> Could not find angle parameter: CA - CB - H4
> Could not find angle parameter: CA - CB - NC
> Could not find angle parameter: CB - NC - CB
> Could not find angle parameter: H4 - CB - NC
> Could not find angle parameter: H4 - CB - NC
> There are missing parameters.
> Unit is OK.
>
> I have attached my PYA.mol2 file, I am getting more confusing with
> the atom types ...
> what should I use for C8, C9, C10, C11 and C12 and for their H atoms ... ?
> any suggestions?
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- application/octet-stream attachment: PYA.mol2
Received on Wed Dec 07 2011 - 02:00:03 PST
