Hello all,
https://pubs.acs.org/doi/full/10.1021/acs.jcim.5b00674
https://pubs.acs.org/doi/suppl/10.1021/acs.jcim.5b00674/suppl_file/ci5b00674_si_001.pdf
I guess my error coming from this part (I am not so sure)
.<TRIPOS>MOLECULE
LIG
52 52 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 N 144.1030 198.5620 176.9400 n3 0 LIG
-0.701600
2 N1 141.3350 198.1970 175.9020 n3 0 LIG
-0.711600
3 N2 140.5480 196.7460 178.3670 n3 0 LIG
-0.774600
4 N3 143.3260 197.1060 179.4180 n3 0 LIG
-0.711600
5 O 144.9280 195.9750 177.2280 o 0 LIG
-0.871800
6 O1 143.2880 196.5480 174.8890 o 0 LIG
-0.869550
7 O2 141.0920 195.2010 176.1420 o 0 LIG
-0.622100
.......................................................................................................................
When I change the name of LIG as a RES -everything is fine. (I saw the RES
name in the second example in the zip file (
https://pubs.acs.org/doi/full/10.1021/acs.jcim.5b00674)
but I didn't clearly understand the "naa_mol2files" )
So my question
Is RES a general name for ligand part or How can I write valid general name
for the ligand part?
I hope I am clear.
I looking forward to your answers.
Cheers
Işılay
ışılay öztürk <isilayozturk.gmail.com>, 13 Eki 2022 Per, 00:12 tarihinde
şunu yazdı:
> Dear all,
> Dear all,
>
> I have some problem about using *MCPB.py. *
> https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
> https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm
>
> I am trying to apply these tutorials to my structure. but It is always
> giving to this error: Traceback (most recent call last):
> File "/usr/local/amber20/bin/MCPB.py", line 581, in <module>
> raise pymsmtError('%s is required in naa_mol2files but not '
> pymsmt.exp.pymsmtError: LIG is required in naa_mol2files but not provided.
>
> If I am not wrong "2naa_mol2files " is defining to my ligand part.
>
> So How can I fix this problem?
>
> Thank you in advance
>
> Best,
>
> Işılay
>
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Received on Wed Oct 12 2022 - 15:30:02 PDT
