AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jun 11 2008 - 09:57:59 CDT

Hi:
Still unsuccessful in loading cleanly the combined (stripped) mdcrd
files to VMD.
Described here is what I did, should someone be so patient to check
for mistakes.

I have a number of prmtop files, corresponding to the various steps. I
have now tried the two most naked ones, from docking the ligand onto
the protein with DOCK6.2. Here, a prmtop was for flex scoring, the
other one from amber score in implicit medium, that is, WAT only
appears in the prmtop as the last residue after all protein residues.
I deleted WAT from either one of these two prmtop files and tried with
VMD with the combined mdcrd, stripped of :WAT :POP, and nobox. Result:
highly distorted protein and ligand at each snapshot.

Surely there are other combinations of mdcrd/prmtop. Those I tried
(all other prmtop files - from embedding into the lipidic membrane -
contain WAT BOX and result from 'solvate box model# TIP3Box 12.0') led
to similarly distorted snapshots. I assume that I missed the right
choice of combinations. Before trying other ones, it would help to
appreciate where the above procedure is in error.

Thanks a lot
francesco pietra

On Tue, Jun 10, 2008 at 10:03 AM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> 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.
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>>>
>>>
>>>
>>> --
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>>
>>
>>
>> --
>> Dr Francesco Pietra
>> Professor of Chemistry
>> Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
>> Palazzo Ducale
>> 55100 Lucca (Italy)
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-- 
Dr Francesco Pietra
Professor of Chemistry
Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
Palazzo Ducale
55100 Lucca (Italy)
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