AMBER Archive (2009)

Subject: Re: [AMBER] problem with FAD in tleap

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Nov 30 2009 - 13:25:15 CST

Shahid,

> I also checked on just fad and there is a strange character 'Y' in the
> output pdb:
>
> -bash-3.2$ ambpdb -p fad.top < fad.crd
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 11/30/09 Time = 19:27:07
> REMARK
> ATOM 0 Y FAD 4 0.000 0.000 0.000
> ATOM 1 O3B FAD 4 58.127 139.363 12.551
> ATOM 2 H3T FAD 4 58.026 140.041 11.896
> ATOM 3 C1B FAD 4 56.137 136.961 12.309
> .............the rest is ok.

What is this atom 0 ?

                 LEaP ambpdb
You did: .mol2 -> .top & .crd -> .pdb

If the PDB file is wrong this means the .top & consequently the .mol2
files have errors - or there is a bug in ambpdb...

Do you have the same problem if you use the savepdb command in LEaP ?

regards, Francois

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