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Problem on neutralizing the N- and C-terminal Val
#25736 11/05/10 06:16 PM
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CHING Offline OP
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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
Mechanical Engineering
joint with Biochemistry
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

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