AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jun 19 2009 - 00:41:54 CDT

Michael,

> Thank you for the detailed advice.

Please, read about the P2N file format:
See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
   as well as
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php

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

Here is a part of my .cshrc file:
----------------------
setenv SOFT /usr/local

setenv GAMESS_SCR /usr/local/0QM_SCR
setenv GAUSS_SCRDIR /usr/local/0QM_SCR
setenv PCGAMESS_SCRDIR /usr/local/0QM_SCR
setenv AMBERHOME /usr/local/amber10

setenv g03root /usr/local
source /usr/local/g03/bsd/g03.login

set path = ($path $SOFT/bin $SOFT/g03 $SOFT/gamess $SOFT/pcgamess
$AMBERHOME/exe)
------------------------

regards, Francois

> -----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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber