From: Brian Radak (
Date: Tue Apr 10 2018 - 09:41:54 CDT

Yes - the problem, more or less, is that between the PDB and CHARMM IC
table there is too much information for psfgen to figure things out. I just
wanted to be sure there was not some special usage of mutate that would
cleverly do the mapping for me.

Deleting the coordinates is about as equally hands-on (but certainly more
elegant) than what I did with pdbalias. If I needed to script this for
multiple sidechains, that sounds like the best route.

We might be able to improve/automate this in future versions of psfgen
if/when we get the maximum common substructure routines implemented.


On Tue, Apr 10, 2018 at 10:23 AM, Jérôme Hénin <> wrote:

> Hi Brian,
> I would expect the internal coordinates usually included in CHARMM
> topologies to be enough to reconstruct a full side chain with a likely
> geometry, from nothing but the backbone. Could it be that those coordinates
> that are present (CB, HB1, HB2) are incompatible with the internal
> coordinates? In this case my safest approach would be to delete all
> sidechain coordinates except CB, and let ICs provide the others.
> Jerome
> On 10 April 2018 at 15:58, Brian Radak <> wrote:
>> The user guide is unfortunately lacking in good examples for this.
>> I have a simple, complete peptide structure for (ALA)_5 and want to make
>> a new PSF/PDB with psfgen after converting the central residue (resid 3) to
>> ASP. The mutate command sounds perfect for this. I did something like the
>> following:
>> segment PROA {
>> pdb foo.pdb
>> mutate 3 ASP
>> }
>> coordpdb foo.pdb PROA
>> guesscoord
>> which works, but predictably has trouble reading the PDB since it finds
>> the atom HB3 in ALA when it is expecting CG, etc. from ASP. The guessed
>> coordinates for the added carboxylate are fairly atrocious with a
>> completely unphysical dihedral. Is this an expected limitation of mutate?
>> Obviously it is a bit too much to ask that mutate immediately figure out
>> the mapping between those two atoms on-the-fly. I was able to tell psfgen
>> about that mapping by adding:
>> pdbalias atom ALA HB3 CG
>> before reading coordinates, but I'm pretty sure this is a global mapping
>> that discards the HB3 coordinates for all other ALA residues (not what I
>> want). This works out just fine in my case, but seems unsatisfying as the
>> solution to the problem in general. Is there a more specific workaround
>> than this? What would I do for a more complicated mutation like LYS to TYR?
>> Cheers,
>> Brian