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#196 - 10/21/04 06:28 PM Problem solved [Re: Edo]
Edo Offline
Forum Member

Registered: 08/31/04
Posts: 192
Hi,
It appears the problem was I was running a parrallel compiled vesion of charmm, instead of the serial version.

When I run the serial version the scripts seem to work fine.

Thanks for your time and help,
Ed

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#197 - 10/22/04 10:39 AM Re: Problem solved [Re: Edo]
zhangxd68 Offline
Forum Member

Registered: 10/31/03
Posts: 39
hi, ED

The inputfile is your input file name, not just the "****.pdb". You misunderstand.

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#198 - 05/17/05 04:10 PM create a big water box: solvent-box.str and readwat-box.str [Re: lennart]
guan Offline
Forum Member

Registered: 04/27/05
Posts: 74

The templete solvent-box.str was used. Anybody has comments on the following?

size 35x35x95 is Ok, but 45x45x95 gives error:

CHARMM> read sequence tip3 @NSLAB
Parameter: NSLAB -> "1944"

CHARMM> gene wat3 noangle nodihe
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
GENPSF> Segment 5 has been generated. Its identifier is ^@^@^@^@^@^@^@^@.


***** LEVEL -4 WARNING FROM *****
***** DATA STRUCTURE REALLOCATED IN ALLDT
******************************************
BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5

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#199 - 05/17/05 04:31 PM Re: create a big water box: solvent-box.str and readwat-box.str [Re: guan]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
The size of the system that can be created using these scripts depends on the size parameter used when CHARMM was installed at your site. To resolve this you have to re-install CHARMM using eg LARGE or XXLARGE. Note that even if the final number of atoms/residues could be handled by your present CHARMM version, the scripts may still fail at an intermediate stage when water molecules are being added. This issue has been discussed before.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#200 - 05/24/07 06:17 PM fortran [Re: lennart]
KdeFuego Offline
Forum Member

Registered: 05/15/07
Posts: 4
what fortran version I must use for make scrips?

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#201 - 05/25/07 02:43 AM Re: fortran [Re: KdeFuego]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
FORTRAN is usually used to make "programs", not scripts. If you are modifying CHARMM source code FORTRAN77 is the standard for versions before c33b1. For c33b1 and later versions use FORTRAN90.
Tip: Use the POST function instead of REPLY when creating a post on a new topic.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#202 - 11/13/08 10:58 AM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
ardie Offline
Forum Member

Registered: 03/28/08
Posts: 43
Hi lennart,
Thanks for your sharing scripts. I am a beginner for charmm. Your scripts really benifit me much. But I have some questions for solvent-shell.str. I think I need your helps. In the DO_X part in solvent-shell.str, you write:

! do the same slab again, but translated -1A and rotated 30 degrees around the x-axis
read sequence tip3 @NSLAB
gene wat3 noangle nodihe
coor dupl sele segid wat0 end sele segid wat3 end
coor rota xdir 1.0 phi 30.0 sele segid wat3 end
coor transl xdir -1.0 sele segid wat3 end

I don't clearly understand why make the slab translated -1A and rotated 30 degrees around the x-axis. Why not just let the slab slide along the x-axisdo without "translated -1A and rotated 30 degrees around the x-axis" ?

Thanks.

Ardie

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#203 - 11/13/08 11:06 AM Re: Sample scripts for basic tasks in CHARMM [Re: ardie]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
Just to increase the chance that we fill all possible cavities and crevices with water; there may be low density regions in the water box we started from.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#204 - 11/14/08 06:51 AM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
ardie Offline
Forum Member

Registered: 03/28/08
Posts: 43
Thanks. But I am still confused. Why do you rotate it by just 30 rather than by other value?


Edited by ardie (11/14/08 06:52 AM)

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#205 - 11/14/08 07:01 AM Re: Sample scripts for basic tasks in CHARMM [Re: ardie]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
If I had picked any other value you could still have asked the same question, so perhaps the number 30 is not so special.
You can change it to any other value that better suits your mood, or remove that part of the script if you want.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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