AMBER Archive (2008)

Subject: Re: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file?

From: Jack Lei (leiming72_at_gmail.com)
Date: Mon Jan 28 2008 - 08:35:06 CST

Thanks. Steve. It works as you said.

I really appreicate your very helpful comments on this.

About protonate command, just double check it. There is no CYM info in
PROTON_INFO file.

Sincerely yours
Jack

On Jan 28, 2008 9:47 PM, Steve Spronk <spronk_at_umich.edu> wrote:

> The problem lies in the fact that your PDB file has an atom called H in
> the CYM amide bond (which is the standard for every other amino acid
> residue), whereas LEaP is expecting an atom named HN (look at atom 5 of the
> library definition). So when LEaP encounters the H in your file, it creates
> a new atom that has not been defined yet. This is a little surprising. I
> am not sure if there was some special motivation for having this unusual
> atom name for CYM in particular.
>
>
>
> Simply changing the H in your PDB file to HN should fix the problem. This
> is an easy fix if you only have to do this occasionally. But then you'll
> always have to change CYM residues to have an HN atom instead of H before
> you load the PDB files into LEaP, which could be a nuisance if you have to
> do it often.
>
>
>
> A better long-term solution is to create a local copy of all_amino94.lib
> and all_amino94.in, changing the name of this HN atom back to H, in line
> with convention. You also would create a local copy of leaprc.ff94 (or
> whatever forcefield you're using), changing the parts where it says "loadOff
> all_amino94.lib" to "loadOff /path/to/new/all_amino94.lib" When you use
> "source" to load the forcefield parameters, use this local copy of
> leaprc.ff94.
>
>
>
> In my opinion, the best solution, if you have the appropriate permissions,
> is to modify all_amino94.lib in the $AMBERHOME area, changing the HN of CYM
> to H to be consistent with the standard convention. Just be sure that the
> other users of Amber on your system, who may have CYM residues in their
> simulations, are aware of this change so that you don't confuse them. To
> me, this one sounds like the best solution, but again, I'm not sure if there
> was some special motivation for making the atom name be HN for CYM.
>
>
>
> Steve
>
>
> ------------------------------
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Jack Lei
> *Sent:* Monday, January 28, 2008 8:00 AM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: Why LEap created a new H atom for CYM while generating
> TOPOLOGY file?
>
>
>
> Dear Ambers:
>
> I am generating a topology file for a protein including CYM residue using
> AMBER8 LEap.
> The CYM ff is listed in all_amion94.in as following:
> -----------------------------------------------------------------
> CYSTEINE with negative charge
>
> CYM INT 1
> CORR OMIT DU BEG
> 0.00000
> 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000
> 2 DUMM DU M 1 0 -1 1.449 0.000 0.000
> 3 DUMM DU M 2 1 0 1.522 111.100 0.000
> 4 N N M 3 2 1 1.335 116.600 180.000
> 5 HN H E 4 3 2 1.010 119.800 0.000
> 6 CA CT M 4 3 2 1.449 121.900 180.000
> 7 HA H1 E 6 4 3 1.090 109.500 300.000
> 8 CB CT 3 6 4 3 1.525 111.100 60.000
> 9 HB3 H1 E 8 6 4 1.090 109.500 60.000
> 10 HB2 H1 E 8 6 4 1.090 109.500 300.000
> * 11 SG S E 8 6 4 1.810 116.000 180.000*
> 12 C C M 6 4 3 1.522 111.100 180.000
> 13 O O E 12 6 4 1.229 120.500 0.000
>
> CHARGE
> -.4157 .2719 -.0351 .0508 -.2413
> .1122 .1122 -.8844 .5973 -.5679
>
> IMPROPER
> -M CA N HN
> CA +M C O
>
> DONE
> ----------------------------------------------------------------------
>
> There is no hydrogen like HG linked with SG in this file.
>
> However, when I generated top file, I got the following unreasonable
> log infomation:
> -----------------------------------
> Loading PDB file: ./A_prot_mod.pdb
> *Created a new atom named: H* within residue: .R<CYM 290>
> .....
> Checking Unit.
> FATAL: Atom .R<CYM 290>.A<H 11> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> -----------------------------------
>
> I doubt that the atom type of SG in CYM caused the problem. Therefore I
> changed
> SG's type (SH) to S in CYM in all_amino94.lib and all_amino94.in. But I
> got the same
> log information. It is clear that there should be no hydrogen created to
> link with SG.
>
> Anyone can explain this?
>
> Another thing, I found there was something wrong with CYM while
> protonating
> CYM (Add wrong H atom). Just add CYM comment to correct it in PROTON_INFO
> file.
>
> My CYM file is listed as following:
> ************************************************
> ATOM 6281 N CYM A 290 -5.529 -11.167 -4.529
> ATOM 6282 H CYM A 290 -4.658 -11.630 -4.747
> ATOM 6283 CA CYM A 290 -5.560 -9.708 -4.626
> ATOM 6284 HA CYM A 290 -5.914 -9.300 -3.702
> ATOM 6285 C CYM A 290 -6.447 -9.197 -5.780
> ATOM 6286 O CYM A 290 -6.550 -9.846 -6.822
> ATOM 6287 CB CYM A 290 -4.116 -9.267 -4.851
> ATOM 6288 3HB CYM A 290 -3.821 -9.609 -5.824
> ATOM 6289 2HB CYM A 290 -3.511 -9.746 -4.105
> ATOM 6290 SG CYM A 290 -3.781 -7.504 -4.771
> *************************************************
>
> Many thanks in advance!
>
> Sincerely yours
> Jack
>

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