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From: Hayden Eastwood <s0237717.sms.ed.ac.uk>

Date: Mon, 30 Apr 2007 12:35:23 +0100

Dear Amber users

I am performing 1NS of constant PH dynamics on a small, highly charged (+11)

peptide of 45 residues. I set up the initial input pdb file as stated in the

amber manual (i.e. I changed ASP to AS4, GLU to GL4). The constant pH ran

without problem. However, when I performed analysis on the output using

calcpka.pl I got the following message:

Can't call method "ResName" on an undefined value at

/opt/amber9/exe/calcpka.pl line 65.

When I looked at the resulting output from calcpka.pl nothing seemed to be

particularly wrong, except that I saw output from 10 residues and not the

expected 11. I also got this line:

GL4 28: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0

Is the implication of this result that I should perform a more extended

dynamics run? How come there is no "predicted pka given" in the above

mentioned output?

My full calcpka.pl output is this:

LYS 8: Offset 2.465 Pred 9.465 Frac Prot 0.997 Transitions 144

TYR 9: Offset 2.167 Pred 9.167 Frac Prot 0.993 Transitions 254

TYR 10: Offset 1.638 Pred 8.638 Frac Prot 0.978 Transitions 430

LYS 26: Offset 2.935 Pred 9.935 Frac Prot 0.999 Transitions 34

GL4 27: Offset -3.886 Pred 3.114 Frac Prot 0.000 Transitions 8

GL4 28: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0

LYS 32: Offset 1.540 Pred 8.540 Frac Prot 0.972 Transitions 788

LYS 39: Offset 1.987 Pred 8.987 Frac Prot 0.990 Transitions 240

LYS 44: Offset 2.580 Pred 9.580 Frac Prot 0.997 Transitions 76

LYS 45: Offset 3.004 Pred 10.004 Frac Prot 0.999 Transitions

42

I would really appreciate some feedback on the matter.

Many thanks

Hayden Eastwood

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Received on Wed May 02 2007 - 06:07:15 PDT

Date: Mon, 30 Apr 2007 12:35:23 +0100

Dear Amber users

I am performing 1NS of constant PH dynamics on a small, highly charged (+11)

peptide of 45 residues. I set up the initial input pdb file as stated in the

amber manual (i.e. I changed ASP to AS4, GLU to GL4). The constant pH ran

without problem. However, when I performed analysis on the output using

calcpka.pl I got the following message:

Can't call method "ResName" on an undefined value at

/opt/amber9/exe/calcpka.pl line 65.

When I looked at the resulting output from calcpka.pl nothing seemed to be

particularly wrong, except that I saw output from 10 residues and not the

expected 11. I also got this line:

GL4 28: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0

Is the implication of this result that I should perform a more extended

dynamics run? How come there is no "predicted pka given" in the above

mentioned output?

My full calcpka.pl output is this:

LYS 8: Offset 2.465 Pred 9.465 Frac Prot 0.997 Transitions 144

TYR 9: Offset 2.167 Pred 9.167 Frac Prot 0.993 Transitions 254

TYR 10: Offset 1.638 Pred 8.638 Frac Prot 0.978 Transitions 430

LYS 26: Offset 2.935 Pred 9.935 Frac Prot 0.999 Transitions 34

GL4 27: Offset -3.886 Pred 3.114 Frac Prot 0.000 Transitions 8

GL4 28: Offset -Inf Pred -Inf Frac Prot 0.000 Transitions 0

LYS 32: Offset 1.540 Pred 8.540 Frac Prot 0.972 Transitions 788

LYS 39: Offset 1.987 Pred 8.987 Frac Prot 0.990 Transitions 240

LYS 44: Offset 2.580 Pred 9.580 Frac Prot 0.997 Transitions 76

LYS 45: Offset 3.004 Pred 10.004 Frac Prot 0.999 Transitions

42

I would really appreciate some feedback on the matter.

Many thanks

Hayden Eastwood

-----------------------------------------------------------------------

The AMBER Mail Reflector

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To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed May 02 2007 - 06:07:15 PDT

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