Re: [gmx-users] Problem in making index.ndx and disres.itp
On 3/16/15 9:17 AM, Tushar Ranjan Moharana wrote: Hi Justine, As you can see in my .itp file the atom number starts from 1. Even this is the case with index file. I tried to modify index file to have atomic number same as pdb file but it gave a blank output. So my first concern is how GROMACS will know which atom I want to restrain? shall I change the atom number in itp file to corresponding atom number in pdb? Topology numbering is based on the [moleculetype], not the global numbers in the coordinate file. You shouldn't adjust anything. -Justin My second concern is the second line of my .itp file looks different from the one given in GROMACS website As per GROMACS website: ; ai aj type index type’ low up1 up2 fac in my generated itp: ; i j ? label funct loup1up2 weight So what do you suggest me to do? Thanks in advance. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in making index.ndx and disres.itp
Hi Justine, As you can see in my .itp file the atom number starts from 1. Even this is the case with index file. I tried to modify index file to have atomic number same as pdb file but it gave a blank output. So my first concern is how GROMACS will know which atom I want to restrain? shall I change the atom number in itp file to corresponding atom number in pdb? My second concern is the second line of my .itp file looks different from the one given in GROMACS website As per GROMACS website: ; ai aj type index type’ low up1 up2 fac in my generated itp: ; i j ? label funct loup1up2 weight So what do you suggest me to do? Thanks in advance. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in making index.ndx and disres.itp
On 3/16/15 4:36 AM, Tushar Ranjan Moharana wrote: Hi everyone, I wanted to run a distance restricted MD. Since I have many atoms I can't do it manually with a text editor. For that I choose the line corresponding the atom from .pdb file to another text file and rename them as disres.pdb. Then I run the following command to generate disres.itp *gmx genrestr -f disres.pdb -disre -o disres.itp* I got the following out put Which I don't think correct. Please rectify my mistakes Why don't you think it's correct? -Justin My disres.pdb file ATOM936 CG ASP61 -36.433 1.944 57.629 0.7994 1.700 C ATOM937 OD1 ASP61 -37.626 1.784 58.005 -0.8014 1.500 O ATOM938 OD2 ASP61 -35.856 3.065 57.600 -0.8014 1.500 O ATOM 1212 CD2 HIS81 -41.384 3.133 58.251 -0.1141 1.700 C ATOM 1208 CE1 HIS81 -41.090 2.008 60.045 -0.0170 1.700 C ATOM 1211 HE2 HIS81 -39.455 3.044 59.220 0.3911 1.300 H ATOM 1295 CD2 HIS87 -38.577 6.571 57.666 0.1292 1.700 C ATOM 1292 CE1 HIS87 -39.069 5.316 56.005 0.2057 1.700 C ATOM 1294 NE2 HIS87 -39.012 5.303 57.324 -0.5727 1.550 N ATOM 3657 CG ASP 238 -37.842 3.869 61.472 0.7994 1.700 C ATOM 3658 OD1 ASP 238 -37.982 2.630 61.652 -0.8014 1.500 O ATOM 3659 OD2 ASP 238 -37.595 4.399 60.357 -0.8014 1.500 O END My disres.itp file *; distance restraints for SideChain of [ distance_restraints ]; i j ? label funct loup1up2 weight1 2 1 0 1 0.026104 0.226104 1.2261 11 3 1 1 1 0.0261116 0.2261121.22611 11 4 1 2 1 0.412962 0.6129621.61296 11 5 1 3 1 0.424679 0.6246791.62468 11 6 1 4 1 0.2588 0.4588 1.4588 11 7 1 5 1 0.409973 0.6099731.60997 11 8 1 6 10.357780.557781.55778 11 9 1 7 1 0.324584 0.5245841.52458 1110 1 8 1 0.352323 0.5523231.55232 1111 1 9 1 0.336515 0.5365151.53652 1112 110 1 0.284958 0.4849581.48496 12 3 111 1 0.122214 0.3222141.32221 12 4 112 1 0.300036 0.5000361.50004 12 5 113 10.302630.502631.50263 12 6 114 1 0.153161 0.3531611.35316 12 7 115 1 0.389231 0.5892311.58923 12 8 116 1 0.330781 0.5307811.53078 12 9 117 1 0.284293 0.4842931.48429 1210 118 1 0.305142 0.5051421.50514 1211 119 1 0.276073 0.4760731.47607 1212 120 1 0.251726 0.4517261.45173 13 4 121 1 0.456662 0.6566621.65666 13 5 122 1 0.487282 0.6872821.68728 13 6 123 1 0.294685 0.4946851.49469 13 7 124 10.343850.543851.54385 13 8 125 10.323490.523491.52349 13 9 126 1 0.287881 0.4878811.48788 1310 127 1 0.342527 0.5425271.54253 1311 128 10.359650.559651.55965 1312 129 1 0.252203 0.452203 1.4522 14 5 130 1 0.113787 0.3137871.31379 14 6 131 1 0.116054 0.3160541.31605 14 7 132 1 0.347675 0.5476751.54768 14 8 133 1 0.289477 0.4894771.48948 14 9 134 1 0.234584 0.4345841.43458 1410 135 1 0.384379 0.5843791.58438 1411 136 1 0.383668 0.5836681.58367 1412 137 1 0.351603 0.551603 1.5516 15 6 138 1 0.110408 0.3104081.31041 15 7 139 1 0.472676 0.6726761.67268 15 8 140 1 0.459901 0.659901 1.6599 15 9 141 1 0.375173 0.5751731.57517 1510 142 1 0.300614 0.5006141.50061 1511 143 1 0.255373 0.4553731.45537 1512 144 1
[gmx-users] Problem in making index.ndx and disres.itp
Hi everyone, I wanted to run a distance restricted MD. Since I have many atoms I can't do it manually with a text editor. For that I choose the line corresponding the atom from .pdb file to another text file and rename them as disres.pdb. Then I run the following command to generate disres.itp *gmx genrestr -f disres.pdb -disre -o disres.itp* I got the following out put Which I don't think correct. Please rectify my mistakes My disres.pdb file ATOM936 CG ASP61 -36.433 1.944 57.629 0.7994 1.700 C ATOM937 OD1 ASP61 -37.626 1.784 58.005 -0.8014 1.500 O ATOM938 OD2 ASP61 -35.856 3.065 57.600 -0.8014 1.500 O ATOM 1212 CD2 HIS81 -41.384 3.133 58.251 -0.1141 1.700 C ATOM 1208 CE1 HIS81 -41.090 2.008 60.045 -0.0170 1.700 C ATOM 1211 HE2 HIS81 -39.455 3.044 59.220 0.3911 1.300 H ATOM 1295 CD2 HIS87 -38.577 6.571 57.666 0.1292 1.700 C ATOM 1292 CE1 HIS87 -39.069 5.316 56.005 0.2057 1.700 C ATOM 1294 NE2 HIS87 -39.012 5.303 57.324 -0.5727 1.550 N ATOM 3657 CG ASP 238 -37.842 3.869 61.472 0.7994 1.700 C ATOM 3658 OD1 ASP 238 -37.982 2.630 61.652 -0.8014 1.500 O ATOM 3659 OD2 ASP 238 -37.595 4.399 60.357 -0.8014 1.500 O END My disres.itp file *; distance restraints for SideChain of [ distance_restraints ]; i j ? label funct loup1up2 weight1 2 1 0 1 0.026104 0.226104 1.2261 11 3 1 1 1 0.0261116 0.2261121.22611 11 4 1 2 1 0.412962 0.6129621.61296 11 5 1 3 1 0.424679 0.6246791.62468 11 6 1 4 1 0.2588 0.4588 1.4588 11 7 1 5 1 0.409973 0.6099731.60997 11 8 1 6 10.357780.557781.55778 11 9 1 7 1 0.324584 0.5245841.52458 1110 1 8 1 0.352323 0.5523231.55232 1111 1 9 1 0.336515 0.5365151.53652 1112 110 1 0.284958 0.4849581.48496 12 3 111 1 0.122214 0.3222141.32221 12 4 112 1 0.300036 0.5000361.50004 12 5 113 10.302630.502631.50263 12 6 114 1 0.153161 0.3531611.35316 12 7 115 1 0.389231 0.5892311.58923 12 8 116 1 0.330781 0.5307811.53078 12 9 117 1 0.284293 0.4842931.48429 1210 118 1 0.305142 0.5051421.50514 1211 119 1 0.276073 0.4760731.47607 1212 120 1 0.251726 0.4517261.45173 13 4 121 1 0.456662 0.6566621.65666 13 5 122 1 0.487282 0.6872821.68728 13 6 123 1 0.294685 0.4946851.49469 13 7 124 10.343850.543851.54385 13 8 125 10.323490.523491.52349 13 9 126 1 0.287881 0.4878811.48788 1310 127 1 0.342527 0.5425271.54253 1311 128 10.359650.559651.55965 1312 129 1 0.252203 0.452203 1.4522 14 5 130 1 0.113787 0.3137871.31379 14 6 131 1 0.116054 0.3160541.31605 14 7 132 1 0.347675 0.5476751.54768 14 8 133 1 0.289477 0.4894771.48948 14 9 134 1 0.234584 0.4345841.43458 1410 135 1 0.384379 0.5843791.58438 1411 136 1 0.383668 0.5836681.58367 1412 137 1 0.351603 0.551603 1.5516 15 6 138 1 0.110408 0.3104081.31041 15 7 139 1 0.472676 0.6726761.67268 15 8 140 1 0.459901 0.659901 1.6599 15 9 141 1 0.375173 0.5751731.57517 1510 142 1 0.300614 0.5006141.50061 1511 143 1 0.255373 0.4553731.45537 1512 144 1 0.324609 0.5246091.52461 16 7 145 1 0.295291 0.4952911.49529
