Dear all,
Thank you for the reply and i'm sorry for the trouble.
I am still having problem reading in my psf file generated from
CHARMM-GUI using chamber.
I have compared psf file that can be read in without any complaining
error and the one that was failed. There is no different in term of
the format of the file. I attached here both my files (only first 27
lines are shown as the original files are too huge to attach here )
and the error with verbose flag is:
psf step5_assembly.psf 4 FLAGs found in the PSF file headerPSF
EXT
CMAP
CHEQ
PSF file has label PSF Checking for
flag: EXTExamining potential match: PSF Examining potential match:
EXT EXT FoundEXTented file format is being usedPSF Title: *
GENERATED BY CHARMM-GUI (
HTTP://WWW.CHARMM-GUI.ORG) ON JAN, 04. 2012.
PSF Title: * ASSEMBLE PREVIOUSLY GENERATED COMPONENTS (LIPID
BILAYER, PROTEIN, PORE WATER, PSF Title: * DATE: 1/ 4/12
1:10:33 CREATED BY USER: apache <read_atom_data>
natom 61860At line 2690 of file _psfprm.f (unit = 20, file =
'step5_assembly.psf')Fortran runtime error: Bad value during integer
read
and the line from 2680 in _psfprm.f is:
do i=1,natom
! 1 AAL 1 ASN N 54 -0.470000 14.0070 0
read(psf_unit,fmt01) ii, & ! 1
lsegid, & ! AAL
iresid(i), & ! 1
lresat(i), & ! ASN
atom_type(i), & ! N
iac(i), & ! 54
cg(i), & ! -0.47000
amass(i), & ! 14.0070
imove(i) ! 0
line 2690 correspond to imove(i) ! 0
I have checked my psf file, it follows the format of 1 AAL 1 ASN
N 54 -0.470000 14.0070 0
Pls advise.
Thanks and regards,
Colvin
On Thu, Dec 29, 2011 at 12:42 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Dec 29, 2011, colvin wrote:
>>
>> I'm sending this email again and hope to get useful feedback... i need a
>> solution for the problems.
>
> Answers are posted on the amber list as people have the time and knowledge to
> provide a response. Reposting after just a day doesn't really serve a useful
> purpose.
>
> In your particular case, the number of people who might know the answer
> is probably in the range of 0 to 2, and people often are on holiday during the
> last week of the year. One suggestion is to use the -verbose flag to get more
> information about what is happening Also look at lines 388 and 2690 of
> _psfprm.f, which may provide clues about what the program doesn't like.
>
> ...dac
>
>
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Received on Wed Jan 04 2012 - 01:30:02 PST
