> all residues are in upper case. Only the lib name is lower case (cym.lib)
> However, i tried to rename them, i.e cym.lib -> CYM.lib, but the same errors
> came.
>
> Could you please help me again?
All of the volunteers on this list are mostly happy to help out... I will
try to provide some of my common debugging ideas. Others may chime in.
Likely I will need further information to move forward.
In general, after I've loaded up new lib/mol2 files, I often look in LEaP
to see if they were loaded as expected; for this I type "list"... This
shows me all the residues (and force fields) that LEaP knows about. In
this list, you should see the modified residues.
I just performed a LEaP with tleap -f leaprc.ff99SB and with list see:
> list
ACE ALA ARG ASH ASN ASP CALA CARG
CASN CASP CCYS CCYX CGLN CGLU CGLY CHCL3BOX
CHID CHIE CHIP CHIS CILE CIO CLEU CLYS
...
RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX SPF
SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOXTP3
TP4 TP5 TPF TRP TYR VAL WAT
-----
When you do this, do you see your modified residues (i.e. HIZ)? You can
also check an already loaded residue with the "check" command, i.e. "check
HIZ". Here I did this for HIS.
> check HIS
Checking 'HIS'....
Checking parameters for unit 'HIS'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Most errors encountered with modified residues / force fields are a
mismatch between the PDB and loaded residues. If you get an "added new
atom" error, this means the PDB had some atom that LEaP didn't recognize
(i.e. was not in the templates). Culprits: mismatch in RES name and/or
mismatch in ATOM name. For us to debug further, we need more info
(ideally the commands to start up LEaP, the mol2/libs loaded (which you
provided) but we need the libs, and the PDB).
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Received on Mon May 09 2011 - 21:00:04 PDT
