[gmx-users] Re: help with building DNA in gromacs

[Justin Lemkul]

On 1/22/13 2:02 PM, Tom wrote:
> Thanks a lot, Justin!
>
> I names residue names to match the force field's expectations
> But I am still having problem of using amber03.ff.
> This my pdb file:
> _________
> .....
> ATOM     28  H5    DC5   1       2.443  -4.389   1.332  1.00  0.00           H
> *ATOM     29  P     DC    2       7.171  -5.306   6.616  1.00  0.00           P *
> ATOM     30  OP1   DC    2       5.787  -5.066   7.086  1.00  0.00           O
> ....
> __________
>
> When I pdb2gmx, i got Fatal error and choose 1: ( 1: AMBER03 protein, nucleic
> AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003))
> ---------------
> Atom P in residue DC 2 was not found in rtp entry*DC5 *with 28 atoms
> while sorting atoms.
>   error report
> ---------
>
> It seems gmx can not recognize the residue type DC and still used DC5 for residue 2.
> Is there a way to solve this problem?
>

Please post a link to where the .pdb file can be downloaded.

Also, please do not reply to the entire digest.  The archive is already 
hopelessly confusing, but let's not make it any worse.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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