Re: [AMBER] atom types for pyridine II...

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Wed, 7 Dec 2011 10:46:06 +0100

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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Received on Wed Dec 07 2011 - 02:00:03 PST
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