Dear David,
Thank you for your advice. I apologize for not posting the exact error
messages. Unfortunately copy paste does not seem to be working for me in
XLEAP. I'll try to describe in detail what I did:
download PCA.sdf from here: https://www3.rcsb.org/ligand/PCA
antechamber -at amber -i PCA.sdf -fi sdf -o PCA.mol2 -fo mol2 -c bcc -s 2
parmchk2 -i PCA.mol2 -f mol2 -o PCA.frcmod
xleap:
source leaprc.protein.ff14SB
loadamberparams PCA.frcmod
PCA=loadmol2 PCA.mol2
edit PCA: delete -OH from carboxyl group, change charge in C5 atom to
get an overall charge of +1
set PCA tail PCA.1.C5
PEP = sequence {PCA CHIS}
check PEP
"No bond parameter for: -
No bond parameter for: - N
No bond parameter for: -
No bond parameter for: -
....
Can't find angle parameter: - -
Can't find angle parameter: - -
Can't find angle parameter: - - N
Can't find angle parameter: - -
Can't find angle parameter: - N - H
Can't find angle parameter: - N - CX
Can't find angle parameter: - -
Can't find angle parameter: - -
Can't find angle parameter: - -
...
Can't find angle parameter: - - N
There are Missing parameters.
Unit is OK.
On 01/27/2017 03:39 PM, David Case wrote:
> On Fri, Jan 27, 2017, Andreas Tosstorff wrote:
>> I am trying to generate a peptide with three non standard residues: pGlu
>> (aka PCA) - His - Gly
>>
>> I tried generating tha parameter files for PCA in antechamber and then
>> load it into leap.
>>
>> I cannot save the parameter files of the resulting peptide, because
>> several bond, angle and torsion parameters are missing.
> *Which* parameters are missing? (Aside: my usual complaint: users seem
> very wary of posting exact error messages, but the details are often most
> important.)
>
> Did you run parmchk2, which will look for any missing parameters, and generate
> gueses? (This is relevant if the missing parameters involve only gaff atom
> types.)
>
> Or, are the missing parameters between Amber atom types (upper-case atom
> types) and gaff (lower-case atom types)? You may have to find the analogous
> Amber types and enter them by hand into a frcmod file. An alternative, which
> I would recommend for a modified amino acid where the modification is well
> out on the side chain: ask antechamber to use Amber atom types. You may still
> need to manually copy gaff parameters to the corresponding Amber atom types,
> but the backbone behavior will then follow that of the Amber force field you
> are using.
>
> ...good luck...dac
>
>
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--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Fri Jan 27 2017 - 08:00:02 PST
