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Problem on neutralizing the N- and C-terminal Val
#25736 11/05/10 06:16 PM
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Hi everyone,

I have a 30 amino acids peptide need to be neutralized.

Its sequence is VVSQM....SITV

When I used the command nter=NNEU,cter=CNEU,blocked
to neutralize the termini, it complains that
No angle parameters for 5 (NH2 CT1 CT1)
No angle parameters for 877 (CT1 CT1 CD )

Does anyone can help me fix it? Many thanks!

CHINGWAI

Re: Problem on neutralizing the N- and C-terminal Val
CHING #25737 11/05/10 06:44 PM
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I don't believe that "nter=NNEU,cter=CNEU,blocked" is a CHARMM command. However, I get the same error with

read sequ val 5
gener a first nneu last cneu warn

One can probably safely assume transferability from NH2-CT1-CT2 and CT2-CT1-CD angle terms in the parameter file, but the omission suggests that other terms (esp. DIHEhral) may also be missing.


Rick Venable
computational chemist

Re: Problem on neutralizing the N- and C-terminal Val
rmv #25738 11/05/10 07:13 PM
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Dear Rick,

I can also use gener, but the problem is that the NNEU and CNEU doesn't work on Val and Gly, but work on Phe, Gln, Ser.

It really confused me! And the other parameters, such as NTER, CTER,CT3,ACE, work on my peptide. However, what I need are -NH2 and -COOH.

Re: Problem on neutralizing the N- and C-terminal Val
CHING #25740 11/05/10 07:52 PM
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Note that the combined use of NNEU and CNEU is not very physical for a peptide chain; experimentally this situation (neutral termini) is usually achieved using capping groups.
Since your initial post indicates that you are not using CHARMM it may be that you are better off getting help from the support site for the program you use.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Problem on neutralizing the N- and C-terminal Val
lennart #25741 11/05/10 08:02 PM
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Dear Lennart,

Thank you for your reply.

It is true that NNEU and CNEU is not physically reasonable for a peptide. But in my case, the termini are not the true termini. I need to neutralize it as NH2 and COOH before energy minimization. That's why I cannot use other similar parameters.

But do you know why it works on some amino acids such as Phe,GLN,SER but not on others like Valine and Glycine?

CHINGWAI

Re: Problem on neutralizing the N- and C-terminal Val
CHING #25742 11/05/10 08:37 PM
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Probably, as Rick indicated, because for val and gly there are some different atomtypes involved. Simple solution is to add proper capping groups - for minimization this should be OK; minimization is usually not a crucial step in an investigation.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Problem on neutralizing the N- and C-terminal Val
lennart #25743 11/05/10 08:46 PM
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Dear Lennart,

Thank you for your reply. I am now using ACE for N-termini and CT3 for C-termini.

CHINGWAI

Re: Problem on neutralizing the N- and C-terminal Val
CHING #25744 11/05/10 09:34 PM
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The somewhat non-physical (in water) NNEU and CNEU end patches are newer, and apparently were not tested for all possible residue types before being added to the topology file. The missing parameters must be added to par_all22_prot.inp before they can be used with Val.

The Gly residue may also require special handling, as is the case for NTER; the GLYP patch must be used instead, but there's an exception for that in the code, which automatically overrides NTER with GLYP (when FIRST was not specified on the command line).

Using ACE and CT3 is more common, and more thoroughly tested.


Rick Venable
computational chemist

Re: Problem on neutralizing the N- and C-terminal Val
rmv #27071 04/08/11 03:01 AM
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I have the same problem, I want to simulate 2MLT.pdb, but charmm complains and gives me this error:
Error in GENIC residue NH2 was not found

I am using this command: -par blocked,nter=ACE,cter=CT3


Vahid Mirjalili
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Re: Problem on neutralizing the N- and C-terminal Val
hiva #27073 04/08/11 03:17 AM
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That's not a CHARMM command; perhaps you want the MMTSB forum, further down on the main forums page?

It's also not the same problem, since that was solved by using ACE and CT3 patches.


Rick Venable
computational chemist

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
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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
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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
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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
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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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