Re: Queries on patches, GDP-topology

Date: Mon Jul 24 2006 - 14:13:41 CDT

Dear Gumbart,
At the outset, thank you for your reply.

You are right perhaps I must first model the chain B since there are
missing residues. That should follow I do not have to link the segments.

Next, you were mentioning about introducing an NTER and CTER for start of
B1(segment 1 of chain B) and end of B2(segment 2 of chain B), to suggest
chain B(domain of a protein though) since, its a peptide chain by itself
must have its N terminal and c terminal. right ?!!

Further clarifying on GDP topology features, you have suggested me to
create a topology for GDP from known source.
I have to modify these changes in my charmm topology file as well as the
parameter file isnt that so ?!
Is it possible that I could put these topology files(1.protein_na, 2.gdp)
seperately one after the other in psfgen ?!

Kindly confirm.
Ramya Gamini

> 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, 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%2

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