Miles,
I'm afraid I can't help you with these prepgen issues, but I would like to
point out that AMBER now has built-in parameters for a number of
fluorescent protein chromophores. These include EGFP with the CRO
chromophore (and several other fluorescent proteins) that have Tyr and Gly
as the 2nd and 3rd residues and also EBFP with the CR2 chromophore, which
has Ser as the 1st residue. In AmberTools16 you can find the atoms types
for all of these in the xFPchromophores.lib file and modified force field
parameters in frcmod.xFPchromophores file. There is also a leaprc file
that loads these files and sets up some atom types.
The parameters for these xFPs were developed to be modular, so you may be
able to use these atoms types and the frcmod file directly in your
situation. The parameters are meant to work with ff14SB, but they utilize
some atom types from GAFF, which is why the leaprc file needs to do a
little bit more than just load the lib and frcmod files. You will need to
calculate charges for the atoms as these are unique for every situation.
Again, sorry I can't help with prepgen, but if you want any assistance with
atom types, etc. feel free to send me a note directly (off the amber
mailing list).
Cheers,
Brent
On Sat, Nov 19, 2016 at 7:50 PM, Taylor, Miles <taylormi.oregonstate.edu>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor.................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Sun Nov 20 2016 - 07:00:04 PST
