From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jul 23 2006 - 20:11:54 CDT
Are you sure you want to just link two ends that span a gap of 27
residues? That seems like it would be very unnatural. Are the
intervening residues ordered structurally (best guess)? You could
attempt to model them in, which would be relatively easy if they are
unstructured.
I think the default patches might be NTER and CTER. In any case, it
doesn't hurt to specify them explicitly, but make sure those are the
ones you want to use. Also, for consistency, you should apply first
NTER for the first B protein and last CTER for the second B protein.
As for modifying GDP to ADP, what you did should be fine. You could
try searching for GDP topology though or create it yourself by using
the guanine parameters along with the ADP parameters (I would think
it wouldn't be too difficult, but I'm no biochemist :).
As for your water molecules, you should be fine.
On Jul 22, 2006, at 7:36 AM, gamini_at_ncbs.res.in wrote:
> Dear NAMD Users,
> hello.
>
> I am a new user of NAMD and I am having certain difficulities
> while attempting to construct my structure file.
>
> The molecular system I have considered is a GTPase bound to its GEF
> (Guanine exchange factor) along with GDP and mg2+ ion.
>
> I have taken the molecule from PDB; id :1RE0.pdb.
> i) Chain A(resid 18-179)- GTPase
> ii) Chain B(residues 95-217,244-315)- SEC 7 domain (not the complete
> protein) of GEF. It has missing residues(218-243)
> iii)GDP (Guanine di phosphate)
> iv) mg2+ ion
>
> In addition, it has drug BFA and citric acid which I am not
> considering.
>
> I have segmented the PDB file to split for segments.
> However since there are missing residues in chain B , it is being
> segmented in to two; B1(95-217), B2(244-315)
> And so, I have the following pdbs;
> a.pdb, b1.pdb, b2.pdb, gdp.pdb, mg.pdb, water.pdb
>
> My commands using psfgen to construct psf looks as follows:
> *****
> package require psfgen
> topology top_all27_prot_na.inp
>
> pdbalias atom ILE CD1 CD
> pdbalias atom LEU CD1 CD2
> pdbalias atom LEU CD2 CD1
> pdbalias residue HIS HSE
>
> pdbalias atom ADP O5* O5'
> pdbalias atom ADP C5* C5'
> pdbalias atom ADP C4* C4'
> pdbalias atom ADP O4* O4'
> pdbalias atom ADP C3* C3'
> pdbalias atom ADP O3* O3'
> pdbalias atom ADP C2* C2'
> pdbalias atom ADP O2* O2'
> pdbalias atom ADP C1* C1'
>
> pdbalias residue HOH TIP3
> pdbalias atom HOH O OH2
>
> segment A {
> pdb a.pdb
> first NTER
> last CTER
> }
>
> segment B1 {
> pdb b1.pdb
> first none
> last none
> }
> segment B2 {
> pdb b2.pdb
> first none
> last none
> }
>
> patch LINK B1:217 B2:244
>
> segment G {
> pdb gdp.pdb
> first none
> last none
> }
>
> segment MG {
> pdb mg.pdb
> first none
> last none
> }
>
> segment W {
> pdb re0_water.pdb
> auto none
> }
>
> coordpdb a.pdb A
> coordpdb b1.pdb B1
> coordpdb b2.pdb B2
> coordpdb gdp.pdb G
> coordpdb mg.pdb MG
> coordpdb water.pdb W
>
> guesscoord
> writepdb re0.pdb
> writepsf re0.psf
> *****
>
> A. Firstly, I have following queries on patches:
>
> As I understand, I have to put a NTER and CTER for chain A; and
> I need to patch segment B1 and B2 since they are of the same chain
> but are
> segmented (due to missing residues).
>
> I am I using the patches correct ?! If not can anybody explain how
> it has
> to be done?
>
> B. My other query is on GDP.
>
> Since the topology I use(top_all27_prot_na.inp) has described only
> ADP,
> I did some changes so as to mimic ADP for my GDP (since its chemical
> formula is very similar).
>
> I manually changed the GDP residue in the gdp.pdb to ADP (kindly
> note, I
> could not use pdbresidue alias to put GDP as ADP ).
> And included pdbaliases for ADP atom (Pls see my psfgen file above)
>
> Can anybody tell me what other changes have to be included.
> or
> Is there any chamm topology & parameter file that comprises of GDP
> or do
> any of you have other suggestions to handle this?!
>
> C. Lastly, I have included water (hetatms given in pdb),
> I want to do solvation and equilibration in water box.
> can I simply use the structure file created further for solvation
> in water
> box or is there anything, I must be aware of ?!
> Kindly help me understand.
>
> Thanking you in advance.
>
> Sincerely,
> Ramya Gamini
>
>
>
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