Dear Amber,
I am writing to you because I am following this tutorial:
http://ambermd.org/tutorials/basic/tutorial5/
This tutorial uses the CRO chromophore (Ser-Tyr-Gly):
https://www3.rcsb.org/ligand/CRO
While I am instead using the NRQ chromophore (Met-Tyr-Gly):
https://www3.rcsb.org/ligand/NRQ
I am on the step that uses Prepgen to eliminate certain residues and it
continues to fail. Here is the command I am running:
prepgen -i NRQ.ac -o NRQ.prepin -m NRQ.mc -rn NRQ
Also, here is the NRQ.mc file that I created:
HEAD_NAME N1
TAIL_NAME C3
MAIN_CHAIN CA1
MAIN_CHAIN C1
MAIN_CHAIN N3
MAIN_CHAIN CA3
OMIT_NAME H2
OMIT_NAME OXT
OMIT_NAME HXT
PRE_HEAD_TYPE C
POST_TAIL_TYPE N
CHARGE 0.0
It seems that every time I run the file I get this output or a similar
error output:
PRE_HEAD_TYPE is C
POST_TAIL_TYPE is N
Net charge of truncated molecule is 0.00
HEAD_ATOM 1 N1
TAIL_ATOM 22 C3
MAIN_CHAIN 1 1 N1
MAIN_CHAIN 2 6 CA1
MAIN_CHAIN 3 7 C1
MAIN_CHAIN 4 20 N3
MAIN_CHAIN 5 21 CA3
MAIN_CHAIN 6 22 C3
OMIT_ATOM 1 25 H2
OMIT_ATOM 2 24 OXT
OMIT_ATOM 3 41 HXT
Number of mainchain atoms (including head and tail atom): 6
Segmentation fault (core dumped)
Prepgen seems to be adding the "MAIN_CHAIN 1 1 N1" and "MAIN_CHAIN
6 22 C3" lines with every attempt. I tried removing all Main_Chains
and it still adds them, I tried adding them beforehand and it duplicated
them.
I am having a little difficulty. Please help.
Thank you.
Sincerely,
Miles Taylor
Graduate Student
Physical Chemistry
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Received on Sat Nov 19 2016 - 17:00:03 PST
