Dear all:
After running cgenff, I was able to build the str file based on mol2 file. Then I started to set up the molecule crd file based on cgenff manual using the script download from the website, which has the following command in the input file:

write coor card name @resi_temp.crd
system "`echo ./mol2crd @RESI_temp.crd @RESI.mol2 @RESI_init.pdb | awk '{print tolower($0)}'`"
read coor pdb name @resi_init.pdb

The program can generate as2_init.pdb file without any problem, but could not generate correct as2.crd file, and I always got the following error message:

CHARMM> system "`echo ./mol2crd @RESI_temp.crd @RESI.mol2 @RESI_init3.pdb | awk '{print tolower($0)}'`"
Parameter: RESI -> "AS2"
Parameter: RESI -> "AS2"
Parameter: RESI -> "AS2"
Invoking: `echo ./mol2crd AS2_temp.crd AS2.mol2 AS2_init3.pdb | awk '{print tolower($0)}'`

CHARMM> read coor pdb name @resi_init3.pdb
Parameter: RESI -> "AS2"
VOPEN> Attempting to open::as2_init3.pdb::
read CHARMM-pdb format
SPATIAL COORDINATES BEING READ FROM UNIT 90
TITLE> *
** WARNING ** After reading, there are no coordinates for selected atom: 1 1 AS2 C1
** WARNING ** After reading, there are no coordinates for selected atom: 2 1 AS2 C2
** WARNING ** After reading, there are no coordinates for selected atom: 3 1 AS2 C3
** WARNING ** After reading, there are no coordinates for selected atom: 4 1 AS2 C4
** WARNING ** After reading, there are no coordinates for selected atom: 5 1 AS2 C5
** WARNING ** After reading, there are no coordinates for selected atom: 6 1 AS2 C6
** WARNING ** After reading, there are no coordinates for selected atom: 7 1 AS2 C7
** WARNING ** After reading, there are no coordinates for selected atom: 8 1 AS2 C8
** WARNING ** After reading, there are no coordinates for selected atom: 9 1 AS2 C9
** WARNING ** After reading, there are no coordinates for selected atom: 10 1 AS2 C10

I am wondering what is wrong. I pasted the head of the str file below:

* Toppar stream file generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
* For use with CGenFF version 3.0.1
* Some parametrs were optimized using VMD FFTK as per following reference ###
* C.G. Mayne, J. Saam, K. Schulten, E. Tajkhorshid,
* J.C. Gumbart. J. Comput. Chem. 2013, 34, 2757-2770.
*

read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
* using valence-based bond orders
*
36 1

! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.


!MASS 501 CG2RA3 12.01070 C !
!MASS 502 CG2RA2 12.01070 C !
!MASS 507 SG2R59 32.06000 S !

default first none last none

RESI AS2 0.000 ! param penalty= 12.000 ; charge penalty= 11.289
GROUP ! CHARGE CH_PENALTY
ATOM C1 CG301 -0.006 ! 20.867
ATOM C2 CG2R61 0.006 ! 17.878
ATOM C3 CG2R61 0.003 ! 7.847
ATOM C4 CG311 -0.101 ! 6.653
ATOM C5 CG311 -0.086 ! 6.312
ATOM C6 CG321 -0.187 ! 8.191
ATOM C7 CG331 -0.267 ! 9.295
ATOM C8 CG321 -0.176 ! 7.236
......


I am wondering what I should do in order to solve the problem. Thank you.

lqz

This makes no sense to me.

You apparently have a PSF and coordinates, since you write coordinates to AS2_temp.crd in the first of the three lines of input that you decided to show us.

Why do you then want to read the same coordinates from a PDB-file?
Did you actually have any coordinates to start with?

That error can be caused by name mismatches between the PSF and the coordinate file; the SEGID, RESID, RESN, etc. must be the same.

let me to be more specific. Although one crd file (as2_init.crd) can be made by the mol2crd program based on mol2 file, the charmm can not write out any coordinates correctly when I asked it to write out new crd file, or pdb file.

The following is the content copied from the minimize.inp file:

set resi AS2
ioformat extended

read rtf card name top_all36_cgenff.rtf
read para card flex name par_all36_cgenff.prm
stream as2.str

read sequence @resi 1
bomlev -1
generate @resi first none last none setup warn
bomlev 1

write coor card name @resi_temp.crd
system "`echo ./mol2crd @resi_temp.crd @resi.mol2 @resi_init.pdb | awk '{print tolower($0)}'`"
read coor pdb name @resi_init.pdb

print coor

......


the as2_temp.crd has all the coordinates as 9999.000, and print coor showed all coordinates as 9999.000 as well.

What makes you think mol2crd can create a coordinate file in PDB format? The directions for its use suggest otherwise.

But you have not read any coordinates, have you?

Thank you very much for helping! It worked.