AMBER Archive (2009)

Subject: Re: [AMBER] Problem with CAP residues

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Apr 07 2009 - 06:01:35 CDT

Dear Susana,

> I am having the following error when I try to load my pdb file with
> CAP residues:

I guess you use LEaP.

> Error: name mismatch: ACE in the library do not have atom H1

Look at the name of your 6 H atoms: H1, H2 and H3.
The ACE & NME libraries contain the HH31, HH32 and HH33 names.
=> You have to rename in your PDB file the name of these six hydrogens
according to the names present in the force field libraries...

I think you will have to rename the HA1 and HA2 Glycine hydrogens as well.

regards, Francois

> This is my pdb file:
>
> Thank you,
>
> Susana
>
> HEADER
> COMPND
> SOURCE
> ATOM 1 CH3 ACE 1 0.000 0.000 0.000
> ATOM 2 C ACE 1 0.000 0.000 1.510
> ATOM 3 O ACE 1 1.029 0.000 2.166
> ATOM 4 H1 ACE 1 1.056 0.000 -0.341
> ATOM 5 H2 ACE 1 -0.498 0.932 -0.341
> ATOM 6 H3 ACE 1 -0.498 -0.932 -0.341
> ATOM 7 N GLY 2 -1.236 0.000 2.027
> ATOM 8 CA GLY 2 -1.447 0.000 3.472
> ATOM 9 C GLY 2 -2.510 -0.993 3.879
> ATOM 10 O GLY 2 -3.570 -1.099 3.284
> ATOM 11 H GLY 2 -2.026 0.000 1.381
> ATOM 12 1HA GLY 2 -0.503 -0.281 3.984
> ATOM 13 2HA GLY 2 -1.779 1.008 3.798
> ATOM 14 N NME 3 -2.154 -1.723 4.944
> ATOM 15 CH3 NME 3 -3.048 -2.740 5.491
> ATOM 16 H NME 3 -1.240 -1.548 5.362
> ATOM 17 H1 NME 3 -2.566 -3.225 6.365
> ATOM 18 H2 NME 3 -3.261 -3.503 4.714
> ATOM 19 H3 NME 3 -3.999 -2.264 5.810
> END
>
>
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>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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