AMBER Archive (2009)

Subject: RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid

From: Brothers, Michael Charles (mcbroth_at_sandia.gov)
Date: Thu Jun 18 2009 - 16:01:52 CDT

Thank you for the detailed advice.

The last problem I'm having (for now) is figuring out where I define the Scratch Directory. Is it in the RED-vIII program?

Thanks (from someone who is just learning this program and is very appreciative).

Mike

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of FyD
Sent: Thursday, June 18, 2009 12:56 PM
To: AMBER Mailing List
Subject: RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid

Dear Mike,

> I've finally got everything set up to run RED-vIII.2, but for some
> reason it won't recognize the fact that I have PC-GAMESS installed
> and not GAMESS. I'm running through the bash shell and have a path
> set to the directory containing pcgamess.exe.

If you want to use PC-GAMESS, just set $QMSOFT = "PC-GAMESS"; line 3631 (end of the code)

> Thank you for your previous help, and hopefully this is just a small
> oversight on my behalf.

Concerning your P2N fie:
Your residue names were not correct: Residue names have to follow the residue numbers. Then, in a same residue two atoms cannot have two identical atom names.
Please, read about the PDB format: See http://www.wwpdb.org/docs.html

I corrected your PDB file (before creation of the p2n file format using Ante_R.E.D.):
For instance:
ATOM 1 CM ACE 1 -2.330 -4.834 1.670
ATOM 2 HM1 ACE 1 -1.818 -4.561 2.617
ATOM 3 HM2 ACE 1 -3.425 -4.848 1.852
ATOM 4 HM3 ACE 1 -2.001 -5.850 1.368
ATOM 5 C ACE 1 -2.022 -3.863 0.566
ATOM 6 O ACE 1 -2.600 -4.067 -0.643
ATOM 7 N CYY 2 -1.229 -2.856 0.769
ATOM 8 H CYY 2 -0.727 -2.792 1.669
ATOM 9 CA CYY 2 -0.831 -1.998 -0.341
ATOM 10 HA CYY 2 -1.718 -1.781 -0.981
ATOM 11 C CYY 2 0.259 -2.680 -1.144
ATOM 12 O CYY 2 1.398 -3.056 -0.507
ATOM 13 CB CYY 2 -0.336 -0.648 0.200
ATOM 14 HB1 CYY 2 -1.109 -0.210 0.866
ATOM 15 HB2 CYY 2 0.595 -0.783 0.791
ATOM 16 SG CYY 2 -0.030 0.506 -1.129
ATOM 17 N1 AMA 3 2.834 2.708 -0.807
ATOM 18 C2 AMA 3 2.076 3.470 -1.623
ATOM 19 O2 AMA 3 2.572 4.513 -2.328
ATOM 20 C3 AMA 3 0.621 3.143 -1.572
ATOM 21 H31 AMA 3 0.041 4.041 -1.265
ATOM 22 H32 AMA 3 0.275 2.785 -2.566
ATOM 23 C4 AMA 3 0.564 2.061 -0.484
ATOM 24 H4 AMA 3 -0.060 2.391 0.374
ATOM 25 C5 AMA 3 1.997 1.943 -0.074
ATOM 26 O5 AMA 3 2.396 1.266 1.028
ATOM 27 C1 ACT 4 4.108 3.186 -0.277
ATOM 28 H11 ACT 4 4.745 3.555 -1.111
ATOM 29 H12 ACT 4 4.666 2.341 0.183
ATOM 30 C2 ACT 4 3.932 4.184 0.647
ATOM 31 O21 ACT 4 3.685 3.849 1.941
ATOM 32 O22 ACT 4 3.899 5.508 0.217
ATOM 33 N1 AMB 5 3.767 6.301 1.301
ATOM 34 C2 AMB 5 4.875 6.961 1.694
ATOM 35 O2 AMB 5 6.120 6.472 1.487
ATOM 36 C3 AMB 5 4.625 8.367 2.127
ATOM 37 H31 AMB 5 4.826 8.480 3.213
ATOM 38 H32 AMB 5 5.248 9.071 1.534
ATOM 39 C4 AMB 5 3.142 8.545 1.807
ATOM 40 H41 AMB 5 2.547 8.754 2.721
ATOM 41 H42 AMB 5 2.991 9.342 1.047
ATOM 42 C5 AMB 5 2.778 7.213 1.242
ATOM 43 O5 AMB 5 1.645 7.004 0.531
ATOM 44 N NME 6 0.100 -2.911 -2.409
ATOM 45 H NME 6 -0.751 -2.584 -2.891
ATOM 46 CM NME 6 1.178 -3.507 -3.171
ATOM 47 HM1 NME 6 0.853 -3.655 -4.223
ATOM 48 HM2 NME 6 2.065 -2.837 -3.168
ATOM 49 HM3 NME 6 1.449 -4.498 -2.748

Using Ante_R.E.D., you get then the following P2N file format:
REMARK
REMARK TITLE MOLECULE
REMARK CHARGE-VALUE 0
REMARK MULTIPLICITY-VALUE 1
REMARK
ATOM 1 CT1 ACE 1 -2.330 -4.834 1.670 CM
ATOM 2 H1 ACE 1 -1.818 -4.561 2.617 HM1
ATOM 3 H1 ACE 1 -3.425 -4.848 1.852 HM2
ATOM 4 H1 ACE 1 -2.001 -5.850 1.368 HM3
ATOM 5 C2 ACE 1 -2.022 -3.863 0.566 C
ATOM 6 O3 ACE 1 -2.600 -4.067 -0.643 O
ATOM 7 N4 CYY 2 -1.229 -2.856 0.769 N
ATOM 8 H4 CYY 2 -0.727 -2.792 1.669 H
ATOM 9 C5 CYY 2 -0.831 -1.998 -0.341 CA
ATOM 10 H5 CYY 2 -1.718 -1.781 -0.981 HA
ATOM 11 C6 CYY 2 0.259 -2.680 -1.144 C
ATOM 12 O7 CYY 2 1.398 -3.056 -0.507 O
ATOM 13 CT8 CYY 2 -0.336 -0.648 0.200 CB
ATOM 14 H8 CYY 2 -1.109 -0.210 0.866 HB1
ATOM 15 H8 CYY 2 0.595 -0.783 0.791 HB2
ATOM 16 S9 CYY 2 -0.030 0.506 -1.129 SG
ATOM 17 N10 AMA 3 2.834 2.708 -0.807 N1
ATOM 18 C11 AMA 3 2.076 3.470 -1.623 C2
ATOM 19 O12 AMA 3 2.572 4.513 -2.328 O2
ATOM 20 CT13 AMA 3 0.621 3.143 -1.572 C3
ATOM 21 H13 AMA 3 0.041 4.041 -1.265 H31
ATOM 22 H13 AMA 3 0.275 2.785 -2.566 H32
ATOM 23 C14 AMA 3 0.564 2.061 -0.484 C4
ATOM 24 H14 AMA 3 -0.060 2.391 0.374 H4
ATOM 25 C15 AMA 3 1.997 1.943 -0.074 C5
ATOM 26 O16 AMA 3 2.396 1.266 1.028 O5
ATOM 27 CT17 ACT 4 4.108 3.186 -0.277 C1
ATOM 28 H17 ACT 4 4.745 3.555 -1.111 H11
ATOM 29 H17 ACT 4 4.666 2.341 0.183 H12
ATOM 30 C18 ACT 4 3.932 4.184 0.647 C2
ATOM 31 O19 ACT 4 3.685 3.849 1.941 O21
ATOM 32 O20 ACT 4 3.899 5.508 0.217 O22
ATOM 33 N21 AMB 5 3.767 6.301 1.301 N1
ATOM 34 C22 AMB 5 4.875 6.961 1.694 C2
ATOM 35 O23 AMB 5 6.120 6.472 1.487 O2
ATOM 36 CT24 AMB 5 4.625 8.367 2.127 C3
ATOM 37 H24 AMB 5 4.826 8.480 3.213 H31
ATOM 38 H24 AMB 5 5.248 9.071 1.534 H32
ATOM 39 CT25 AMB 5 3.142 8.545 1.807 C4
ATOM 40 H25 AMB 5 2.547 8.754 2.721 H41
ATOM 41 H25 AMB 5 2.991 9.342 1.047 H42
ATOM 42 C26 AMB 5 2.778 7.213 1.242 C5
ATOM 43 O27 AMB 5 1.645 7.004 0.531 O5
ATOM 44 N28 NME 6 0.100 -2.911 -2.409 N
ATOM 45 H28 NME 6 -0.751 -2.584 -2.891 H
ATOM 46 CT29 NME 6 1.178 -3.507 -3.171 CM
ATOM 47 H29 NME 6 0.853 -3.655 -4.223 HM1
ATOM 48 H29 NME 6 2.065 -2.837 -3.168 HM2
ATOM 49 H29 NME 6 1.449 -4.498 -2.748 HM3
CONECT 1 2 3 4 5
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1 6 7
CONECT 6 5
CONECT 7 5 8 9
CONECT 8 7
CONECT 9 7 10 11 13
CONECT 10 9
CONECT 11 9 12 44
CONECT 12 11
CONECT 13 9 14 15 16
CONECT 14 13
CONECT 15 13
CONECT 16 13 23
CONECT 17 18 25 27
CONECT 18 17 19 20
CONECT 19 18
CONECT 20 18 21 22 23
CONECT 21 20
CONECT 22 20
CONECT 23 16 20 24 25
CONECT 24 23
CONECT 25 17 23 26
CONECT 26 25
CONECT 27 17 28 29 30
CONECT 28 27
CONECT 29 27
CONECT 30 27 31 32
CONECT 31 30
CONECT 32 30 33
CONECT 33 32 34 42
CONECT 34 33 35 36
CONECT 35 34
CONECT 36 34 37 38 39
CONECT 37 36
CONECT 38 36
CONECT 39 36 40 41 42
CONECT 40 39
CONECT 41 39
CONECT 42 33 39 43
CONECT 43 42
CONECT 44 11 45 46
CONECT 45 44
CONECT 46 44 47 48 49
CONECT 47 46
CONECT 48 46
CONECT 49 46
END

If you want to generate a central fragment for this amino acid, you just modify this P2N file into:
REMARK
REMARK TITLE YOUR-TITLE
REMARK CHARGE-VALUE 0 # If 0 line not required
REMARK MULTIPLICITY-VALUE 1 # If 1 line not required
REMARK
REMARK INTRA-MCC 0.0 | 1 2 3 4 5 6 | remove REMARK INTRA-MCC 0.0 | 44 45 46 47 48 49 | remove REMARK REMARK REORIENT 7 9 11 | 11 9 7 | 7 9 13 | 13 9 7 REMARK
ATOM 1 C1 ACE 1 -2.330 -4.834 1.670 CM # Modified
ATOM 2 H111 ACE 1 -1.818 -4.561 2.617 HM1 #
ATOM 3 H112 ACE 1 -3.425 -4.848 1.852 HM2 #
ATOM 4 H113 ACE 1 -2.001 -5.850 1.368 HM3 #
ATOM 5 C2 ACE 1 -2.022 -3.863 0.566 C
ATOM 6 O3 ACE 1 -2.600 -4.067 -0.643 O
ATOM 7 N4 CYY 2 -1.229 -2.856 0.769 N
ATOM 8 H4 CYY 2 -0.727 -2.792 1.669 H
ATOM 9 C5 CYY 2 -0.831 -1.998 -0.341 CA
ATOM 10 H5 CYY 2 -1.718 -1.781 -0.981 HA
ATOM 11 C6 CYY 2 0.259 -2.680 -1.144 C
ATOM 12 O7 CYY 2 1.398 -3.056 -0.507 O
ATOM 13 CT8 CYY 2 -0.336 -0.648 0.200 CB
ATOM 14 H8 CYY 2 -1.109 -0.210 0.866 HB1
ATOM 15 H8 CYY 2 0.595 -0.783 0.791 HB2
ATOM 16 S9 CYY 2 -0.030 0.506 -1.129 SG
ATOM 17 N10 AMA 3 2.834 2.708 -0.807 N1
ATOM 18 C11 AMA 3 2.076 3.470 -1.623 C2
ATOM 19 O12 AMA 3 2.572 4.513 -2.328 O2
ATOM 20 CT13 AMA 3 0.621 3.143 -1.572 C3
ATOM 21 H13 AMA 3 0.041 4.041 -1.265 H31
ATOM 22 H13 AMA 3 0.275 2.785 -2.566 H32
ATOM 23 C14 AMA 3 0.564 2.061 -0.484 C4
ATOM 24 H14 AMA 3 -0.060 2.391 0.374 H4
ATOM 25 C15 AMA 3 1.997 1.943 -0.074 C5
ATOM 26 O16 AMA 3 2.396 1.266 1.028 O5
ATOM 27 CT17 ACT 4 4.108 3.186 -0.277 C1
ATOM 28 H17 ACT 4 4.745 3.555 -1.111 H11
ATOM 29 H17 ACT 4 4.666 2.341 0.183 H12
ATOM 30 C18 ACT 4 3.932 4.184 0.647 C2
ATOM 31 O19 ACT 4 3.685 3.849 1.941 O21
ATOM 32 O20 ACT 4 3.899 5.508 0.217 O22
ATOM 33 N21 AMB 5 3.767 6.301 1.301 N1
ATOM 34 C22 AMB 5 4.875 6.961 1.694 C2
ATOM 35 O23 AMB 5 6.120 6.472 1.487 O2
ATOM 36 CT24 AMB 5 4.625 8.367 2.127 C3
ATOM 37 H24 AMB 5 4.826 8.480 3.213 H31
ATOM 38 H24 AMB 5 5.248 9.071 1.534 H32
ATOM 39 CT25 AMB 5 3.142 8.545 1.807 C4
ATOM 40 H25 AMB 5 2.547 8.754 2.721 H41
ATOM 41 H25 AMB 5 2.991 9.342 1.047 H42
ATOM 42 C26 AMB 5 2.778 7.213 1.242 C5
ATOM 43 O27 AMB 5 1.645 7.004 0.531 O5
ATOM 44 N28 NME 6 0.100 -2.911 -2.409 N
ATOM 45 H28 NME 6 -0.751 -2.584 -2.891 H
ATOM 46 C29 NME 6 1.178 -3.507 -3.171 CM # modified
ATOM 47 H291 NME 6 0.853 -3.655 -4.223 HM1 #
ATOM 48 H292 NME 6 2.065 -2.837 -3.168 HM2 #
ATOM 49 H293 NME 6 1.449 -4.498 -2.748 HM3 #
CONECT 1 2 3 4 5
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1 6 7
CONECT 6 5
CONECT 7 5 8 9
CONECT 8 7
CONECT 9 7 10 11 13
CONECT 10 9
CONECT 11 9 12 44
CONECT 12 11
CONECT 13 9 14 15 16
CONECT 14 13
CONECT 15 13
CONECT 16 13 23
CONECT 17 18 25 27
CONECT 18 17 19 20
CONECT 19 18
CONECT 20 18 21 22 23
CONECT 21 20
CONECT 22 20
CONECT 23 16 20 24 25
CONECT 24 23
CONECT 25 17 23 26
CONECT 26 25
CONECT 27 17 28 29 30
CONECT 28 27
CONECT 29 27
CONECT 30 27 31 32
CONECT 31 30
CONECT 32 30 33
CONECT 33 32 34 42
CONECT 34 33 35 36
CONECT 35 34
CONECT 36 34 37 38 39
CONECT 37 36
CONECT 38 36
CONECT 39 36 40 41 42
CONECT 40 39
CONECT 41 39
CONECT 42 33 39 43
CONECT 43 42
CONECT 44 11 45 46
CONECT 45 44
CONECT 46 44 47 48 49
CONECT 47 46
CONECT 48 46
CONECT 49 46
END

R.E.D. fully handles multiple residue names in the Tripos mol2 file format...

For terminal fragments, you will need Methylamonium and/or acetate as well.

regards, Francois

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]
> On Behalf Of FyD
> Sent: Wednesday, June 10, 2009 11:48 PM
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] Generating LeAP file for helix containing
> non-standard amino acid
>
> Dear Michael,
>
>> I am having issues generating an amber force field for a protein
>> containing my non-standard amino acid. I generated the helix itself
>> in Macromodel and then modified the amino acid to my side chain
>> (Cysteine -> Cys + side-chain, labeled DMV in this model).
>
> When you want to develop a force field library for a new amino-acid,
> you first need to decide which type of FF library you wish to build:
> N-terminal, C-terminal or a central fragment.
> (Usually, you only need the central fragment).
>
> You could follow what is provided @
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
> Central fragment:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
>
> N-terminal fragment:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
>
> C-terminal fragment:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
>
> and the three together:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>
> In all the cases, you need to prepare a capped amino-acid (AA), such
> as ACE-AA-NME, and you cannot use the PDB file you sent.
>
> Examples of similar approaches are available in R.E.DD.B.
> See http://q4md-forcefieldtools.org/REDDB/projects/F-81/
> http://q4md-forcefieldtools.org/REDDB/projects/F-82/
> http://q4md-forcefieldtools.org/REDDB/projects/F-73/
>
> regards, Francois

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