VMD-L Mailing List

From: Gaurav Sharma (sharma_at_coe.neu.edu)
Date: Tue Feb 15 2005 - 17:13:16 CST

Hi Ludwig,

I used the following commands to protonate the D residues:

segment A { pdb gcn4A.pdb }
patch ASPP A:7
coordpdb gcn4A.pdb A
guesscoord
writepsf ....
writepdb ....

But, my final pdb file still lists the D residues as ASP and not as ASPP
!! though I am sure it gets protonated since there is an added hydrogen
atom in the new residue. I have appended the portion of the pdb files
which contain the residue before and after using the patch command:

before patch:
ATOM 109 N ASP 7 32.702 19.646 9.977 1.00 0.00 A
ATOM 110 HN ASP 7 33.572 19.269 10.284 1.00 0.00 A
ATOM 111 CA ASP 7 32.448 19.407 8.572 1.00 0.00 A
ATOM 112 HA ASP 7 32.315 20.381 8.116 1.00 0.00 A
ATOM 113 CB ASP 7 33.610 18.684 7.924 1.00 0.00 A
ATOM 114 HB1 ASP 7 33.925 17.843 8.574 1.00 0.00 A
ATOM 115 HB2 ASP 7 33.313 18.272 6.939 1.00 0.00 A
ATOM 116 CG ASP 7 34.776 19.591 7.745 1.00 0.00 A
ATOM 117 OD1 ASP 7 34.733 20.818 7.831 1.00 0.00 A
ATOM 118 OD2 ASP 7 35.858 18.890 7.598 1.00 0.00 A
ATOM 119 C ASP 7 31.148 18.623 8.330 1.00 0.00 A
ATOM 120 O ASP 7 30.375 18.963 7.441 1.00 0.00 A

after patch:
ATOM 114 CB ASP 7 33.610 18.684 7.924 1.00 0.00 A
ATOM 115 HB1 ASP 7 33.925 17.843 8.574 0.00 0.00 A
ATOM 116 HB2 ASP 7 33.313 18.272 6.939 0.00 0.00 A
ATOM 117 CG ASP 7 34.776 19.591 7.745 1.00 0.00 A
ATOM 118 OD1 ASP 7 34.733 20.818 7.831 1.00 0.00 A
ATOM 119 OD2 ASP 7 35.858 18.890 7.598 1.00 0.00 A
ATOM 120 HD2 ASP 7 36.644 19.507 7.567 0.00 0.00 A
ATOM 121 N ASP 7 32.702 19.646 9.977 1.00 0.00 A
ATOM 122 HN ASP 7 33.572 19.269 10.284 0.00 0.00 A
ATOM 123 CA ASP 7 32.448 19.407 8.572 1.00 0.00 A
ATOM 124 HA ASP 7 32.315 20.381 8.116 0.00 0.00 A
ATOM 125 C ASP 7 31.148 18.623 8.330 1.00 0.00 A
ATOM 126 O ASP 7 30.375 18.963 7.441 1.00 0.00 A

Are you sure the residue name changes after applying patch command ?

Regards,
Gaurav

Luis Rosales wrote:

>Hi:
>
>If you have D & E protonated, they are defined as ASPP and GLUP on your
>pdb/psf, right??
>
>I think that you will need to:
>
>1. save a new pdb without hydrogens
>2. generate a new psf file using aliases:
>
>alias residue GLUP GLU
>alias residue ASPP ASP
>
>Now you have unprotonated D & E residues!!!
>Dont forget to write new pdb/psf files...
>
>Hope this helps,
>
>Ludwig
>
>
>
>--
>Open WebMail Project (http://openwebmail.org)
>
>
>---------- Original Message -----------
>From: Gaurav Sharma <sharma_at_coe.neu.edu>
>To: vmd-l_at_ks.uiuc.edu
>Sent: Tue, 15 Feb 2005 11:42:06 -0500
>Subject: vmd-l: Unprotonating GLU, ASP
>
>
>
>>Hi All,
>>
>>I used the psfgen's patch command to protonate GLU, ASPs to study
>>the effect of lower pH. Is there a similar patch command to un-
>>protonate the GLU, ASP in the final structure obtained from the
>>above simulation in order to study the reversibility of the reaction.
>>
>>Thanks in advance,
>>
>>Gaurav
>>
>>
>------- End of Original Message -------
>
>