AMBER Archive (2008)

Subject: Re: AMBER: Combine mdcrd while stripping WAT problem

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 10 2008 - 03:03:02 CDT

whether you say nobox depends on whether your new
stripped prmtop (and you must make one) has a box or
not. just be consistent and it should be ok.
distortions come from the mdcrd and prmtop not
have the same amount of data per frame, either
from mismatch in natom or mismatch in box presence.
calros

On Tue, Jun 10, 2008 at 3:37 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> Hi:
> Perhaps you also refer to discussion I took part to last year for the
> same problem with Amber9.
>
> Like at that time, docking of the ligand was now carried out (DOCK6.2)
> with the protein embodying a single molecule of water of
> crystallization. That is, the prmtop corresponding to protein+ligand
> before embedding into the membrane contains that WAT. I already tried
> the WAT&POP stripped mdcrd with that prmtop. Did not work, i.e., both
> the protein and the ligand looked like heavily distorted at each
> snapshot when loading to VMD the stripped mdcrd file.
>
> I can try again with prmtop stripped (with text editor) of that WAT,
> although as carried out above it did not work. Before doing that, a
> question: is it meaningful to command 'nobox' while stripping only WAT
> (and not POP too)?
>
> Thanks for the suggestions.
> francesco pietra
>
> On Sun, Jun 8, 2008 at 9:33 PM, Carlos Simmerling
> <carlos.simmerling_at_gmail.com> wrote:
>> also, if you strip water, you might want to use the "nobox"
>> flag after trajout so that box coordinate are not written. by default
>> they are. if you use the correct prmtop corresponding to the
>> stripped system, try loading the trajectory in VMD using the
>> coordinates with box and see if it helps. there is lots of
>> discussion of this in the archives.
>>
>> On Sun, Jun 8, 2008 at 2:58 PM, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:
>>> On Sun, Jun 8, 2008 at 11:40 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>>> With Amber10, on accumulating ns of trajectory, I am facing a problem
>>>> of trajectory analysis unresolved since Amber9 for the same protein
>>>> and environment, though for a different ligand.
>>>>
>>>> The system is a large protein, carrying a large non-peptidic ligand.
>>>> It is embedded in a POP, TIP3P hydrated, membrane. Everything flows
>>>> correctly, 39% faster with pmemd with respect to sander.MPI.
>>>>
>>>> What I am trying to do with ptraj is combining *.mdcrd while stripping WAT
>>>>
>>>> While a complete action would be:
>>>>
>>>> trajin prod1.mdcrd.gz
>>>> trajin prod2.mdcrd.gz
>>>> ......................
>>>> trajout prod1-#_no_wat.mdcrd nobox
>>>> strip :WAT
>>>> strip :POP
>>>>
>>>> I tried simply:
>>>>
>>>> trajin prod1.mdcrd.gz
>>>> trajin prod2.mdcrd.gz
>>>> ......................
>>>> trajout prod1-#_no_wat.mdcrd
>>>> strip :WAT
>>>>
>>>> That in view of using the *.prmtop for MD and in order not to change
>>>> the residue numbering.
>>>>
>>>> With the same *.prmtop used for MD, the combined file does not load
>>>> cleanly with VMD. As expected.
>>>
>>> What exaclty do you mean by "not load cleanly"? Do you get any error
>>> messages? Anyways, I'm not sure it could ever load correctly, since
>>> after stripping the waters the number of atoms in the prmtop file is
>>> different than in the prod1-#_no_wat.mdcrd file.
>>>
>>>> I removed all WAT from *.prmtop. The same problem.
>>>
>>> I suppose there's more to it than just removing the "WAT" residues.
>>> You may want to take a look into the 'rdparm' utility, described
>>> together with ptraj. (Check the "stripwater" and then "writeparm"
>>> commands).
>>>
>>> Gustavo.
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>> to majordomo_at_scripps.edu
>>>
>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>
>
>
> --
> Dr Francesco Pietra
> Professor of Chemistry
> Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
> Palazzo Ducale
> 55100 Lucca (Italy)
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu