February 2005 - modeller_usage

SO4 ion coordinates not written
by Cheri M Turman 02 Feb '05

02 Feb '05

I did have both: SET HETATM_IO = on, WATER_IO = on However, the water coordinates were generated and also my heme hetatm had generated coordinates. The SO4s were the only ones that didn't work. This is why I am thinking it has something to do with the settings in restyp.lib. Any other ideas? Cheri > Hi fellow modellers, > I am trying to model my protein with SO4 included in the template pdb > file. My problem first started when I used # for sulfate ion in my .ali > file but MODELLER stopped early with an error where it was trying to > match up the SO4 with GLYP. I thought this was probably because # is > used for GLYP in the restyp.lib file and it is the first one defined in > the list with a #. Therefore, I changed # to s for SO4 (also changed > the original s for sarcosine to #). The model was produced but no > coordinates were written for sulfate ions. Does anyone know what I > might need to do to get the coordinates written? Cheri SET HETATM_IO=on This allows the 'HETATM' groups to be written to the model file. j. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Cheri M. Turman Graduate Student University of Texas-Houston Medical School 6431 Fannin Houston, TX 77030 USA e-mail: cheri.m.turman(a)uth.tmc.edu Ph.: 713-500-6126 Fax: 713-500-0652

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SO4 ion coordinates not written
by Cheri M Turman 01 Feb '05

01 Feb '05

Hi fellow modellers, I am trying to model my protein with SO4 included in the template pdb file. My problem first started when I used # for sulfate ion in my .ali file but MODELLER stopped early with an error where it was trying to match up the SO4 with GLYP. I thought this was probably because # is used for GLYP in the restyp.lib file and it is the first one defined in the list with a #. Therefore, I changed # to s for SO4 (also changed the original s for sarcosine to #). The model was produced but no coordinates were written for sulfate ions. Does anyone know what I might need to do to get the coordinates written? Cheers, Cheri ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Cheri M. Turman Graduate Student University of Texas-Houston Medical School 6431 Fannin Houston, TX 77030 USA e-mail: cheri.m.turman(a)uth.tmc.edu Ph.: 713-500-6126 Fax: 713-500-0652

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problem!
by vivek sharma 01 Feb '05

01 Feb '05

Dear Ben, Just let me know if there is anything wrong in this method. I am generating 50 structures for a template and as I told you program crashed with 'Internal Error' message as 'Energy (= NaN)' value gone out of the limits after generating 29 models. As you said to refine the structure before modelling, but I couldn't find a direct method to do that in inbuilt 'model' script, instead, I am generating 10 structures at a time with different RAND_SEED value in each run, therefore running this 5 times (different RAND_SEED values) to get again 50 structures. Is this OK? Yes, program runs fine. Please let me know, if there is any flaw in this procedure as compared to a single run of generation of 50 structures. I will be thankful. thanks and regards, Vivek Sharma --------------------old message--------------- Date: Fri, 28 Jan 2005 19:12:59 +0200 From: vivek sharma <vivek.sharma(a)helsinki.fi> Reply-To: vivek sharma <vivek.sharma(a)helsinki.fi> Subject: problem To: modeller_usage(a)salilab.org Dear Sir, I am a regular user of MODELER and I use 6v2. But now when I was generating 50 structures of a target using some templates, program ran fine till generating first 28 structures but died in 29 structure generation with the error mentioned below (please see below). For, the first time I have observed this error. What can be the problem. In the last statements of optimization schedule in log file you can see the current value of energy is mentioned by 'NaN'. What does this mean, looks like 'energy' has gone out of certain limits. 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 Initial value of energy before optimization : 35818.9410 Current energy : NaN Symmetry term within energy : 0.0000 Optimizer exit status : 1 Number of iterations : 1 Number of calls to energy function : 201 Number of updates of dynamic contacts : 1 Number of non-updates of dynamic contacts : 201 Final maximal atomic shift : 0.000 TOP_________> 7609 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 7610 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 7611 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 7612 238 END_DO TOP_________> 7613 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 7614 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 3854 49753 TOP_________> 7615 234 OPTIMIZE getcell_247E> Internal error: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 55660213 54355.680 53.082 Starting time : 2005/01/28 14:43:47.350 Closing time : 2005/01/28 18:09:34.578 Total CPU time [seconds] : 12315.51 Please have a look to the error, and suggest what can be the reason. I am first time facing such strange error, otherwise MODELER has worked fine always. Regards, Vivek -- VIVEK SHARMA "You must be the change you wish to see in the world." MKG ----- End forwarded message ----- -- VIVEK SHARMA HBG BI "You must be the change you wish to see in the world." MKG

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modelling heterodimer.
by DUVVURU Raja 01 Feb '05

01 Feb '05

Dear all, I am new to such a wonderfull software. i have a question regarding the modeller usage. i want to modell a heterotetramer i.e protein complex formed by two homodimeric proteins. is there any way that i could do it using the modeller. if this is not possible please let me know if there is a way to model homodimers or heterodimers using modeller. thanking you.

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