AMBER Archive (2005)

Subject: RE: AMBER: read pdb back to xleap after solvation of chloroform

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 19 2005 - 20:41:31 CDT

Dear Chaiann

> If I also load chcl3.in then i get this.
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-H1-C1-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes

Just ignore this message, but make sure you load the chcl3.in file BEFORE
you load your pdb file. To check the unit loaded okay you can enter

edit CL3

This should bring up the CHCl3 molecule in the edit window.
You can then load the relevant leaprc.gaff, leaprc.ff03 frcmod.chcl3 and
then finally your pdb file. The CL3 residue should then be recognised. If it
isn't check the names of the atoms in the CL3 residue in your pdb file they
should match those in the chcl3.in file - namely H1, C1, CL1, CL2, CL3 - if
they don't then you will need to edit your pdb file such that the atom names
match.

I hope this helps.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu