Queries on patches, GDP-topology

From: gamini_at_ncbs.res.in
Date: Sat Jul 22 2006 - 07:36:15 CDT

Dear NAMD Users,

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

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.
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.

Ramya Gamini

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