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

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Tue, 6 Dec 2011 11:04:57 +0100

Dear Franocis,

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,
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?
 
/Urszula




________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Dienstag, 6. Dezember 2011 07:36
An: AMBER Mailing List
Betreff: Re: [AMBER] atom types for pyridine ...

Urszula,

Also, I would rename the atom names in the PDB input file before
generating the P2N file with Ante_R.E.D. 2.0 so that these atom names
are automatically added in the mol2 file generated by R.E.D...

See for comparison the atom names in the PHE residue for the aromatic
ring for instance.

Among others, having more conventional atom names simplify the
analyzes of the trajectory when using ptraj (wild card can be used).

regards, Francois


> I have problems with proposing the atom types for the pyridine molecule ...
>
> 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 C8 -1.766459 -0.896904 -0.076042 CA 1 PYA
> 0.1171 ****
> 9 C9 -2.623650 -0.605483 -1.126238 CA 1 PYA
> -0.3646 ****
> 10 H9 -2.321269 -0.760458 -2.146784 HA 1 PYA
> 0.1558 ****
> 11 C10 -2.253978 -0.688025 1.209409 CA 1 PYA
> -0.2597 ****
> 12 H10 -1.651676 -0.902180 2.074037 HA 1 PYA
> 0.1277 ****
> 13 C11 -3.893742 -0.122764 -0.850677 CA 1 PYA
> 0.3138 ****
> 14 H12 -4.569416 0.106050 -1.656600 HA 1 PYA
> 0.0636 ****
> 15 C12 -3.537068 -0.201541 1.372658 CA 1 PYA
> 0.2798 ****
> 16 H11 -3.928313 -0.034089 2.360846 HA 1 PYA
> 0.0689 ****
> 17 N13 -4.350531 0.082106 0.368715 NA 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 ****
>
>
> I have also tried to use CM atom type but still got errors...
>
>> check x
> Checking 'x'....
> Checking parameters for unit 'x'.
> Checking for bond parameters.
> Checking for angle parameters.
> Could not find angle parameter: CA - CA - NA
> Could not find angle parameter: CA - CA - NA
> Could not find angle parameter: CA - NA - CA
> Could not find angle parameter: HA - CA - NA
> Could not find angle parameter: HA - CA - NA
> There are missing parameters.
> Unit is OK.



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Tue Dec 06 2011 - 02:30:03 PST
Custom Search