Thanks a lot for your information. I got following three parts of warnings on the screen:

1)
CHARMM> READ PARAM UNIT 2 CARD

PARAMETER FILE BEING READ FROM UNIT 2
TITLE> *>>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<
TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: www.CHARMM.ORG
TITLE> * PARAMETER SET DISCUSSION FORUM
TITLE> *
PARRDR> WARNING: ATOMS IN HBOND CAP 0.00 -0.07000 1.99240 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND FA 0.00 -0.12000 1.70000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND CN 0.00 -0.20000 1.75000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND NC 0.00 -0.60000 1.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND OCA 0.00 -0.12000 1.70000 DONT EXIST

Those parts are the new parts added into the new par file. I do not know why they were not defined.

2)

**** Warning **** The following extraneous characters
were found while command processing in PARRDR
0.000000 -0.120000 1.400000

I really do not know why that could happen.

3)
PARRDR> WARNING: ATOMS IN HBOND COA 0.00 -0.11000 2.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND CF1 0.00 -0.06000 1.90000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND CF2 0.00 -0.04200 2.05000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND CF3 0.00 -0.02000 2.30000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND HF1 0.00 -0.02800 1.32000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND HF2 0.00 -0.03000 1.30000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND F1 0.0 -0.13500 1.63000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND F2 0.0 -0.10500 1.63000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND F3 0.0 -0.09700 1.60000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND C3 0.00 -0.02000 2.27500 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND CC1A 0.0 -0.06800 2.09000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND CC1B 0.0 -0.06800 2.09000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND CC2 0.0 -0.06400 2.08000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND NS1 0.00 -0.20000 1.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND NS2 0.00 -0.20000 1.85000 DONT EXIST

***** WARNING ***** PARRDR no nonbond parameters for atom type: 16 HF1
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 17 HF2
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 46 CN
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 47 CAP
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 48 COA
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 49 C3
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 61 NC
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 78 OCA
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 87 CF1
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 88 CF2
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 89 CF3
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 92 FA
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 93 F1
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 94 F2
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 95 F3
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 112 CC1A
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 113 CC1B
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 114 CC2
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 120 NS1
NO nonbond interactions will be computed for this atom type.
***** WARNING ***** PARRDR no nonbond parameters for atom type: 121 NS2
NO nonbond interactions will be computed for this atom type.
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.


In fact, I checked the top file, a lot of atom types are defined there. So what is wrong?