Hi,Pengfei!

First, thank you for your patience and kind help, and your help really do me a great favor!

Now, I will present the information about my pdb file briefly and hope you can solve my doubts.


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The protein has a Calcium ion binding site LINKing with 5 Oxygens atom (I only keep one water for it have problems in step 1 and I just want to do the metal parameters building):

1: ASP 160 OD2
2: ASP 161 OD2
3: ASN 224 OD1
4: VAL 226 O
5: TRP 228 O

Unlike the MCPB Amber tutorial A20 (1AMP), Zinc ion links with atoms all locating in the sidechain, in my pdb, 3 of them (160,161,224) are atoms in sidechain, but the other two (VAL TRP) are backbone Oxygen.

Problem 1: 
So, how to calculate the parameters between metal ion and such atom in backbone?

Problem 2:
Below is the sidechain.bcl file I have some modification. Everything works well and reasonable except the VAL and TRP residues. As I say, Oxygen atom in backbone of VAL226 and TRP228 links with metal ion, so, should I still have command "addToResidue /NAME/CLR/VA1 /NAME/1/VAL-226 not bb"??

I guess this sentense means add origin VAL-226 not backbone(bb) to new molecular /NAME/CLR/VA1".
I don't know whether it is suitable for my case about VAL and TRP.

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createResidue AN1 in CLR
addToResidue /NAME/CLR/AN1 /NAME/1/ASN-224 not bb

# Create GL1-4 from GLU-152
createResidue VA1 in CLR
addToResidue /NAME/CLR/VA1 /NAME/1/VAL-226 not bb

# Create HD2-5 from HID-256
createResidue TR1 in CLR
addToResidue /NAME/CLR/TR1 /NAME/1/TRP-228 not bb
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Problem 3:

The same as problem 2:

addFragment terminal/CH3 bd /NAME/CLR/VA1-4/.CB. ag /NAME/CLR/VA1-4/.CG1 tr /NAME/CLR/VA1-4/HG11 120.7
addFragment terminal/CH3 bd /NAME/CLR/TR1-5/.CB. ag /NAME/CLR/TR1-5/.CG. tr /NAME/CLR/TR1-5/.CD1 270.6

I need the Oxygen atom in sidechain in VAL and TRP, so I think replace methyl with CA means backbone has gone. Is it suitable? If not, how can I do?

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Problem 4:
createBond /NAME/CLR/CA1/C0.. /NAME/CLR/VA1/.O..
createBond /NAME/CLR/CA1/C0.. /NAME/CLR/TR1/.O..

This command occurs error when creatbond with Calcium whith Oxygen atoms in backbone. It seems that we can only process sidechain model. But in my case, I need calculate parameter for metal with backbone Oxygen.

Is it my syntax error or just MCPB can only deal with sidechain??

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Others:

In A20 tutorial section 3 (6), in amber official wite:

You say:

mv 1AMP_OH_sidechain_opt.com 1AMP_OH_sidechain_opt_md.com
sed -i 's/_opt/opt_md/g' 1AMP_OH_sidechain_opt_md.com
mv 1AMP_OH_sidechain_fc.com 1AMP_OH_sidechain_fc_md.com
sed -i 's/_fc/_fc_md/g' 1AMP_OH_sidechain_fc_md.com

but whether it is right for this:
mv 1AMP_OH_sidechain_opt.com 1AMP_OH_sidechain_opt_md.com
sed -i 's/_opt/_opt_md/g' 1AMP_OH_sidechain_opt_md.com            (s/_opt/opt_md/g==>s/_opt/_opt_md/g)
mv 1AMP_OH_sidechain_fc.com 1AMP_OH_sidechain_fc_md.com
sed -i 's/_fc/_opt_md/g' 1AMP_OH_sidechain_fc_md.com               (s/_fc/_fc_md/g==>s/_fc/_opt_md/g)

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Finally, thank you again!

And appreciate you if you can give me a sidechain.bcl file modified by youself!

And if I can go through my parameters building successfully, I could make a detail workflow step by step to help others if you'd like.

Yours Sincerely!
Gao






