Dear Dr. Cheatham III,
Thank you very much for your help.
I found the mistakes while loading the lib and using list. I should've put *
HIZ*=loadpdb hiz.pdb (rather than *hiz*=loadpdb hiz.pdb) shown as below.
By the way, this is the lib I created. I attached here in case you need it.
Thank you very much.
*> loadoff HIZ.lib
Loading library: ./HIZ.lib
Loading: hiz
> 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
CMET CPHE CPRO CSER CTHR CTRP CTYR
CVAL
CYM CYS CYX Cl- Cs+ DA DA3
DA5
DAN DC DC3 DC4 DC5 DCN DG
DG3
DG5 DGN DT DT3 DT5 DTN GLH
GLN
GLU GLY HID HIE HIP HIS HOH
IB
ILE K+ LEU LYN LYS Li+ MEOHBOX
MET
MG2 NALA NARG NASN NASP NCYS NCYX
NGLN
NGLU NGLY NHE NHID NHIE NHIP NHIS
NILE
NLEU NLYS NMABOX NME NMET NPHE NPRO
NSER
NTHR NTRP NTYR NVAL Na+ PHE PL3
POL3BOX
PRO QSPCFWBOX RA RA3 RA5 RAN RC
RC3
RC5 RCN RG RG3 RG5 RGN RU
RU3
RU5 RUN Rb+ SER SPC SPCBOX SPCFWBOX
SPF
SPG T4E THR TIP3PBOX TIP3PFBOX TIP4PBOX
TIP4PEWBOXTP3
TP4 TP5 TPF TRP TYR VAL WAT
frcmod99SB
hiz parm99 *
Regards,
Chinh
On Tue, May 10, 2011 at 11:49 AM, Thomas Cheatham <tec3.utah.edu> wrote:
> > 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 Tue May 10 2011 - 01:30:02 PDT
