AMBER Archive (2008)

Subject: 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 - 06:59:38 CST

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu