Re: [gmx-users] genion question
Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? Payman On Tue, 2009-08-25 at 17:22 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: I realized sth about the previous error message I posted. In the following I have copied the lines (with their line number) which grompp gives warning on! in .gro file: 65868 10940SOLHW265866 5.038 5.739 6.407 65869 10940SOL MW65867 5.103 5.710 6.455 65870 10940SOLLP165868 5.061 5.644 6.524 65871 10940SOLLP265869 5.144 5.630 6.405 65872 10941Na Na65870 1.844 0.957 1.889 658735.4 6.23500 10.24600 in .top file: 4147 [ molecules ] 4148 ; Compound#mols 4149 Protein_A 1 4150 SOL 10903 4151 Na+ 1 I have tested that if I remove the + sign, grompp will not work at all and says such molecule does not exists. So, I am not sure where the Na-NA mismatch comes from?! Ion names are force field-specific. If you left -pname as the default, it assigns Na (for ffgmx). Check ions.itp for the correct name. -Justin Payman On Tue, 2009-08-25 at 15:59 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: When I look at the .top file generated by pdb2gmx, the last lines show how this -0.99 is generated: 442 opls_302 37ARG CZ138 0.64 12.011 ; qtot -0.33 443 opls_300 37ARGNH1139 -0.814.0067 ; qtot -1.13 444 opls_301 37ARG HH11139 0.46 1.008 ; qtot -0.67 445 opls_301 37ARG HH12139 0.46 1.008 ; qtot -0.21 446 opls_300 37ARGNH2140 -0.814.0067 ; qtot -1.01 447 opls_301 37ARG HH21140 0.46 1.008 ; qtot -0.55 448 opls_301 37ARG HH22140 0.46 1.008 ; qtot -0.09 449 opls_271 37ARG C1410.7 12.011 ; qtot 0.61 450 opls_272 37ARG O1141 -0.815.9994 ; qtot -0.19 451 opls_272 37ARG O2141 -0.815.9994 ; qtot -0.99 The charged side-chains are Arg, Lys, 2 * Asp and Glu. Since the pH of simulation is supposed to be close to 7.0, I believe one of the negatively-charged side chains needs to be neutralized. That's why I think one Na+ might be helpful. That's probably correct. I just wanted to verify what was in your system. If you just had water, it made no sense. But with a protein involved with lots of partial charges, these rounding issues do occur. You really do have a system with -1 charge. -Justin Payman On Tue, 2009-08-25 at 15:45 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: OK! It worked! Thanks a lot again. But I have a final technical question. After running grompp, it shows that my box has a net charge of -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is OK?! or even this 0.01 charge will cause me troubles? Depending on the size of your system, rounding errors can occur. It is unusual that the hundredths place would be showing this error. Usually you'd get something like 0.8 or something. Your water topology has a zero net charge; is there something else in your system causing the -1 charge? Adding a single Na+ to neutralize the charge may be appropriate, but that's up to you based on what's in your system (something else may be broken, but I just don't know). -Justin Sorry for tons of e-mails. regards, Payman On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: OK! That's fine. But what if I do not have permissions to make such changes in the itp files? Also, isn't that the case that when you define That's why I said copy the force field files into your local directory. Once there, you can modify them. sth for the second time, grompp will take the second one? Sorry for mass of e-mail! That is only true in the case of .mdp files. -Justin Payman On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: I have done that already! I use my local copy to make my files. but how can I get rid of this error? get into the oplsaanb.itp or include this water model in the topology file before oplsaa.itp? I don't understand what you're saying you've already done. The problem is this: when grompp attempts to assemble the .tpr file, it reads all of the information from the ffoplsaa*.itp files. It finds the directives like [defaults], [atomtypes], etc in a pre-defined order. If, later, it finds a duplicate of these directives, it complains. So when you #include your .itp file
Re: [gmx-users] genion question
Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion question
Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion question
Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top to see where things start going wrong (i.e., not an integer). I would think your system would have to be quite large to accumulate such a difference in charge. -Justin Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion question
Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including hydrogens). I am not sure if I can attach the .top file to my e-mail for you to check. This way I could learn where and how things go wrong! Payman On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top to see where things start going wrong (i.e., not an integer). I would think your system would have to be quite large to accumulate such a difference in charge. -Justin Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion question
Well, if I have understood your words properly, apparently there is a problem in the first residue in amino terminal which I treated the NH2 as a zwitterionic piece(+1), and gave the side chain -1 charge. I thought it should add up to zero, but apparently it does not: 1 opls_287 1ASP N 1 -0.314.0067 ; qtot -0.3 2 opls_290 1ASP H1 1 0.33 1.008 ; qtot 0.03 3 opls_290 1ASP H2 1 0.33 1.008 ; qtot 0.36 4 opls_290 1ASP H3 1 0.33 1.008 ; qtot 0.69 5 opls_299 1ASP CA 1 0.15 12.011 ; qtot 0.84 6 opls_140 1ASP HA 1 0.06 1.008 ; qtot 0.9 7 opls_274 1ASP CB 2 -0.22 12.011 ; qtot 0.68 8 opls_140 1ASPHB1 2 0.06 1.008 ; qtot 0.74 9 opls_140 1ASPHB2 2 0.06 1.008 ; qtot 0.8 10 opls_271 1ASP CG 30.7 12.011 ; qtot 1.5 11 opls_272 1ASPOD1 3 -0.815.9994 ; qtot 0.7 12 opls_272 1ASPOD2 3 -0.815.9994 ; qtot -0.1 13 opls_235 1ASP C 40.5 12.011 ; qtot 0.4 14 opls_236 1ASP O 4 -0.515.9994 ; qtot -0.1 What do you think? Payman On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including hydrogens). I am not sure if I can attach the .top file to my e-mail for you to check. This way I could learn where and how things go wrong! The total charge will undoubtedly fluctuate. What's most important to look at is when you reach the end of a residue and you do not see an integer charge. -Justin Payman On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top to see where things start going wrong (i.e., not an integer). I would think your system would have to be quite large to accumulate such a difference in charge. -Justin Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genion question
Paymon Pirzadeh wrote: Well, if I have understood your words properly, apparently there is a problem in the first residue in amino terminal which I treated the NH2 as a zwitterionic piece(+1), and gave the side chain -1 charge. I thought it should add up to zero, but apparently it does not: You chose the wrong terminus. The Zwitterion-NH3+ species is for an isolated amino acid containing both NH3+ and COO- alpha-carbon substituents. Choose a plain NH3+ for your terminus. -Justin 1 opls_287 1ASP N 1 -0.314.0067 ; qtot -0.3 2 opls_290 1ASP H1 1 0.33 1.008 ; qtot 0.03 3 opls_290 1ASP H2 1 0.33 1.008 ; qtot 0.36 4 opls_290 1ASP H3 1 0.33 1.008 ; qtot 0.69 5 opls_299 1ASP CA 1 0.15 12.011 ; qtot 0.84 6 opls_140 1ASP HA 1 0.06 1.008 ; qtot 0.9 7 opls_274 1ASP CB 2 -0.22 12.011 ; qtot 0.68 8 opls_140 1ASPHB1 2 0.06 1.008 ; qtot 0.74 9 opls_140 1ASPHB2 2 0.06 1.008 ; qtot 0.8 10 opls_271 1ASP CG 30.7 12.011 ; qtot 1.5 11 opls_272 1ASPOD1 3 -0.815.9994 ; qtot 0.7 12 opls_272 1ASPOD2 3 -0.815.9994 ; qtot -0.1 13 opls_235 1ASP C 40.5 12.011 ; qtot 0.4 14 opls_236 1ASP O 4 -0.515.9994 ; qtot -0.1 What do you think? Payman On Tue, 2009-08-25 at 18:53 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including hydrogens). I am not sure if I can attach the .top file to my e-mail for you to check. This way I could learn where and how things go wrong! The total charge will undoubtedly fluctuate. What's most important to look at is when you reach the end of a residue and you do not see an integer charge. -Justin Payman On Tue, 2009-08-25 at 18:15 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.itp in the #ifdef _FF_OPLS section: [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 opls_4071 NA+ NA 1 1 22.98977 -pname switch, but again during the grompp I ran into the following error: Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used atom names from AFP_I_solvated_54_62_102_null.gro will be ignored I really do not know what I am doing wrong here! Also regarding past discussions, adding this single ion has lead into the following note: NOTE 1 [file AFP_I.top, line 4151]: System has non-zero total charge: 1.00e-02 I am not sure if that much charge will cause me troubles or not! I am somewhat troubled by the magnitude of charge discrepancy. Look in the .top to see where things start going wrong (i.e., not an integer). I would think your system would have to be quite large to accumulate such a difference in charge. -Justin Payman On Wed, 2009-08-26 at 07:53 +1000, Mark Abraham wrote: Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of decimal numbers on computers can be inexact, such that things like 0.02 added to itself 100 times does not pass a test for equality with 2. You may be observing this kind of thing here. Your protein's [atoms] directive has a running count of the total charge on the molecule - go and read it and see that each residue has an integral charge. Hopefully you can observe where the rounding error might be occurring and you can make a judgement about whether this might be true. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
Re: [gmx-users] genion question
Hi Guys, I have a question. I am using genion to add two ZN2+ ions to a protein that already has two. I thought I would just use genion with np 2. However it seemed to recognize that there were already two in the file and added none. So instead I used the parameter np 4. This seemed to add two, for a total of four, which I wanted. However sometimes it seems to add two too many! Am I understanding the proper use of the np parameter? If it seemed to add two too many, then the most likely cause was that you had fewer ions in your input structure than you thought you had. You should check out the man page for genion, and consider using -pq. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
