AMBER Archive (2008)

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

From: Steve Spronk (spronk_at_umich.edu)
Date: Mon Jan 28 2008 - 07:47:39 CST

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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