Thanks for the suggestion. I tried running all the files through
dos2unix but I still get the same error. However, I didn't get any error
when I placed all the files in the current directory and entered all the
commands manually. I can live with this. There is one more message in
leap which I am worried about. The zinc in the protein is coordinated to
two histidines which I named HIN. On saving prmtop and inpcrd file i get
the following message
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CPHE 1
FAD 1
HIN 2
NTYR 1
ZNB 3
)
(no restraints)
I can understand this happening for the two termini, FAD and Zinc. Can
you please help me in understanding why I get this message for the
histidines?
Regards.
Amin.
On 2014-05-23 17:53, Jason Swails wrote:
> On May 23, 2014, at 2:05 AM, amin.imtech.res.inwrote:
> Dear all, I am trying to use the zinc parameters from Yuan-Ping Pang. I have copied the files into the respective directories. When i try to source leaprc.zinc, I get errors like this : Log file: ./leap.log # # loading force field parameters for the tetrahedraon-shaped zinc divalent cation # addAtomTypes { { "DZ" "Zn" "sp3" } { "Zn" "Zn" "sp3" } }
addAtomTypes: Improper number of arguments! usage: addAtomTypes
<list_of_lists>
>> loadOff znb.lib
Could not open file znb.lib : not found Could not open database:
znb.lib
>> loadOff hin.lib
Could not open file hin.lib : not found Could not open database:
hin.lib
>> loadOff hydroxide.lib
Could not open file hydroxide.lib : not found Could not open database:
hydroxide.lib
>> loadamberparams frcmod.zinc
Could not open file frcmod.zinc : not found
> exit
I have placed the lib files in $AMBERHOME/dat/leap/lib and frcmod file
in $AMBERHOME/dat/leap/parm. I can load the other leaprc files present
in this directory without any problem. Can someone please help me with
this?
Why not put the files in the same directory you are running tleap in?
That said, these errors do not make sense. The addAtomTypes syntax looks
correct, and anything in $AMBERHOME/dat/leap/* should be in the default
search paths for tleap and xleap.
The only possible problem I can imagine is that your file has DOS line
endings (carriage returns, or rn) instead of newlines (just n). If this
is the case, it may be parsing the last character of every command with
a trailing r which would not appear on the screen or error message, but
would prevent files from being found or lists from being terminated.
This is all speculation, though.
Try running every file you downloaded through the dos2unix program
(which modifies files in-place, getting rid of carriage return endings).
For example:
dos2unix znb.lib
dos2unix hin.lib
dos2unix hydroxide.lib
dos2unix frcmod.zinc
dos2unix leaprc.whatever
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 23 2014 - 07:00:02 PDT
