Hi Dave,
here is an example of what I have observed. I want to generate a prepin file
for a
modified amino acid residue, cysteine oxide. Single conformation, single
molecule case,
with the additional constraint that the backbone atoms N,H,C,O have the same
charges as
the other neutral amino acids.
I have used residuegen with the command
residuegen resgen.in > resgen.out
This produces all the files in the attached tar file (cannot zip it otherwise
our mail server complains).
I would like to point your attention to the file RESIDUE_GEN_RESP.OUTPUT1,
where it reads "there
are 1 charge constraints", i.e. the constraint that the capping atoms have a
total charge
of zero is completely ignored.
Now, if I edit the RESIDUE_GEN_RESP.INPUT1 file, remove the blank line after
the atom block,
and save it as RESP_TF.INPUT, and run
resp -O -i RESP_TF.INPUT -o RESP_TF.OUTPUT -q QIN -e cyo.esp
I get the constraint into the resp calculation as desired.
Further tracking this down lead to blaming respgen for producing the resp
input file which contains
the extra blank line as described in one of my earlier posts.
Hope this helps.
All the best,
Th.
Mit freundlichen Grüßen / Kind regards,
Dr. Thomas Fox
Boehringer Ingelheim Pharma GmbH & Co. KG
Dept. Lead Identific. and Optim. Sup. Ge
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585
mailto:thomas.fox.boehringer-ingelheim.com
Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
Ralf Gorniak, Mark Hagmann, Michael Klein, Dr. Martin Wanning; Vorsitzender
des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR B 23260
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Received on Fri Oct 07 2011 - 05:30:03 PDT
