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Re: Problem on neutralizing the N- and C-terminal Val
rmv #27408 05/03/11 09:38 PM
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Rick, thank you for the suggestion,

I actually want to use a charged C-terminus and a neutral N-terminus. Because the N-terminus is located in a hydrophobic region, but the C-terminus is exposed to water.

So, would you please tell me what are the physical patches for charged C-terminal and neutral N-terminal?

When I used the following charmm command, I still get the same error "residue NNEU not found"
generate firs NNEU last CNEU A setup warn

I appreciate your help,


Vahid Mirjalili
Mechanical Engineering
joint with Biochemistry
Re: Problem on neutralizing the N- and C-terminal Val
hiva #27409 05/03/11 09:51 PM
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Perhaps you need a newer version of the protein topology file; that patch was only included with c35b1 and later CHARMM releases.


Also, it's usually best if the segment name is the 2nd word, i.e.

generate A firs NNEU last CNEU setup warn


Rick Venable
computational chemist

Re: Problem on neutralizing the N- and C-terminal Val
rmv #27410 05/03/11 10:15 PM
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Rick,

Thanks, so I used top_all36_prot_lipid.rtf, and the corresponding parameter file. Now, I have the residue but it lacks some of the bonding parameters:

CHARMM> generate A firs NNEU last CNEU setup warn
THE PATCH 'NNEU' WILL BE USED FOR THE FIRST RESIDUE
THE PATCH 'CNEU' WILL BE USED FOR THE LAST RESIDUE
** WARNING ** BOND NOT FOUND FOR RESIDUE 1 GLY .
ATOMS "N " "HN " WERE REQUESTED.
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 1 GLY .
ATOMS "N " "-C " "CA " "HN " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 1 GLY .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** DONOR NOT FOUND FOR RESIDUE 1 GLY .
ATOMS "HN " "N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 26 GLN .
ATOMS "C " "+N " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 26 GLN .
ATOMS "O " "C " WERE REQUESTED.
** WARNING ** IMPROPER NOT FOUND FOR RESIDUE 26 GLN .
ATOMS "C " "CA " "+N " "O " WERE REQUESTED.
** WARNING ** CROSSTERM NOT FOUND FOR RESIDUE 26 GLN .
ATOMS "-C " "N " "CA " "C "
ATOMS "N " "CA " "C " "+N " WERE REQUESTED.
** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 26 GLN .
ATOMS "O " "C " WERE REQUESTED.
<CODES>: No angle parameters for 7 ( HB CT1 HB )
<CODES>: A TOTAL OF 1 MISSING PARAMETERS

***** LEVEL -1 WARNING FROM <CODES> *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( -1) IS REACHED - TERMINATING. WRNLEV IS 5


Vahid Mirjalili
Mechanical Engineering
joint with Biochemistry
Re: Problem on neutralizing the N- and C-terminal Val
hiva #27411 05/03/11 10:19 PM
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This issue may have been addressed earlier in this thread.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Problem on neutralizing the N- and C-terminal Val
lennart #27412 05/03/11 10:35 PM
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Dear Lennart,

Yes, right. ACE for N-terminal works without any problem. But, what is a good patch to use for charged C-terminal?


Vahid Mirjalili
Mechanical Engineering
joint with Biochemistry
Re: Problem on neutralizing the N- and C-terminal Val
lennart #27413 05/03/11 10:38 PM
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It appears that NNEU was also not tested for GLY; it looks like a separate patch for this case may be needed, to handle the different C atom type (CT2 vs. CT1).


Rick Venable
computational chemist

Re: Problem on neutralizing the N- and C-terminal Val
rmv #27414 05/03/11 10:39 PM
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The default CTER patch usually works fine for the charged C-term.


Rick Venable
computational chemist

Re: Problem on neutralizing the N- and C-terminal Val
rmv #27415 05/03/11 11:36 PM
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Thank you all for the information, now I am using the correct patches for N-term and C-term.


Vahid Mirjalili
Mechanical Engineering
joint with Biochemistry
Re: Problem on neutralizing the N- and C-terminal Val
hiva #27418 05/04/11 05:43 PM
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I'd like to add for the record that the parameters for the patches that are "physical" for proteins or peptidic fragments thereof in a reasonable pH range (CT3, CTER, ACE, ACP, NTER, GPLY, PROP) are thoroughly optimized. The same cannot always be said for the other patches; even when the parameters are not missing, they may not be all that good. This even extends to side chain patches; for instance, I've had some trouble with the neutral arginine patch at some point.

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