AMBER Archive (2009)

Subject: [AMBER] Very weird topology problem

From: ranqi zhu (zhuranqi_at_msn.com)
Date: Sat Jan 24 2009 - 15:14:24 CST

Hi, Everyone,

I am having a very weird problem.
I have some trajectory from gromacs simulations and I want to use ptraj in amber10
to cluster them. So the raw idea is:
1. extract pdb from raw xtc file (I can extract amber trj (g87 format) directly actually, but the unit is different from amber which cause trouble, so I extract pdb instead)
2. I need to generate a topology file that is needed by ptraj. I have to use tleap to do this.
So I pick a random pdb from the result of step 1. Since there are some naming convention difference between gromacs pdb and amber pdb, i have to manually change a few of them (For example, HB1,HB2->HB2,HB3). Then the tleap works and I can get a amber topology file.
3. Then using this topology file, I can use ptraj to convert all the PDBs I get from step1 into amber trj files. Then concatenate all the single trajs into a big traj and cluster them. (I did delete first line of single trjs and add a first line after concatenation).
4. I got partially broken representitive structure from the ptraj clustering. The strucutrue shows missing bonds in vmd or pymol. It feels like vmd or pymol has the upper limit for bond length and some atom distance are a little over that, so vmd/pymol refuse to display them. However the oringall PDB from step 1 looks perfect. Representivive strucutre generated from ptraj should be directly chosen from the original structures from step 1 and shouldn't have this problem. So I think the problem is from the pdb->trj procedure.

So, I did some test to pinpoint this problem.

step 1
I geneterate the topology file by the
tleap -f leap.in

the content of leap.in is:

source leaprc.ff99SB
model = loadpdb p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.pdb
saveamberparm model conf_amber.top conf_amber.crd
savepdb model conf_amber.pdb
quit

step 2
Then I have this conf_amber.top. Then I can do the convert by
ptraj conf_amber.top <traj.in>traj.out

The content of traj.in is:

trajin p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.pdb
trajout p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.trj trajectory
step 3
After doing this I got a trj file. Then I convert it back to pdb and problem happens

ptraj conf_amber.top <trajpdb.in>traj.out

The content of trajpdb.in is :
trajin p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.trj 1 1 1

trajout p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.pdb pdb

step 4
after step3 we get a pdb which is
p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.pdb.1

use pymol to compare , pdbs and topology are attached.
p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.pdb,
p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.pdb.1

p53TAD~wt13~RUN0~opls-25-Trjs-protein3654.pdb.1 miss bonds just like the representive structures from
generated by ptraj clustering.

Any idea? The exact same procedure from all the other simulations. Only this one have problem.

Best,
Ranqi

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