Re: [AMBER] error in creating prmtop and inpcrd files

From: Ben Roberts <ben.roberts.geek.nz>
Date: Sun, 13 Mar 2011 17:34:48 -0400

Hi Chris,

On 13/03/2011, at 4:55 PM, Chris Bryant wrote:

> Seems like it is all of them. Here is the file I am working with. Does this answer your question?

Thanks for the clarification. I don't think the problem is all the atoms; for example, in your logs, it complains about ARG 361 HB1, ARG 361 HG1, ARG 361 HD1, etc. Notably, however, HB2, HG2, HD2, etc. don't trigger the same complaint. This is because, for example, LeAP expects hydrogens on CB in ARG residues to be named HB2 and HB3, instead of HB1 and HB2 (and likewise for hydrogens attached to other heavy atoms).

If I understand correctly, LeAP expects very specific atom names in its residues when assigning atom types. If your atoms aren't named according to the entries in the residue topology libraries, it won't be able to address them.

The official atom naming scheme can be found in the file:

$AMBERHOME/dat/leap/lib/all_amino94.lib (for intra-chain amino acids)
$AMBERHOME/dat/leap/lib/all_aminoct94.lib (for C-terminal amino acids)
$AMBERHOME/dat/leap/lib/all_aminont94.lib (for N-terminal amino acids)

One possible approach is to fix the hydrogen atom names by hand (for example, in residue 361, replacing HB1 and HB2 with HB2 and HB3 respectively, and so on). However, I don't recommend this given that it's very time-consuming. Another is to throw away all hydrogen atoms from your PDB and let other programs add them for you. I think leap should be able to add correctly named hydrogen atoms automatically given a heavy-atom skeleton; if not, check out "reduce", which is bundled with AmberTools.

Good luck!

Ben

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Received on Sun Mar 13 2011 - 15:00:03 PDT
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