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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Received on Wed Jan 30 2008 - 06:07:13 PST
