<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><b><span style="font-weight: bold;"></span></b><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br>Ricardo O. S. Soares wrote:<br>> Hello dear users,<br>> <br>> I'm having a problem trying to simulate one trimer. I'm using tip4p water and right after I fill the box with water and try to pre-process (grompp) the resulting .gro and .top, I get the following error:<br>> <br>> <br>> -------------------------------------------------------<br>> Program grompp, VERSION 4.5.1<br>> Source code file: grompp.c, line: 377<br>> <br>> Fatal error:<br>> number of coordinates in coordinate file (../box/box_water.gro, 274045)<br>>
does not match topology (../top_water.top, 273029)<br>> For more information and tips for troubleshooting, please check the GROMACS<br>> website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>> -------------------------------------------------------<br>> <br>> Here's the ending of the .top file:<br>> <br>> [ molecules ]<br>> ; Compound #mols<br>> Protein_chain_A 1<br>> Protein_chain_H 1<br>> Protein_chain_L 1<br>> SOL 59<br>> SOL 97<br>> SOL 98<br>> SOL 66032<br>> <br>> And the beginning of the .gro file shows the number "274045"<br>>
<br>><br>><br>>>The .top specifies fewer atoms than the .gro, so it's possible that there was some problem when genbox wrote the topology. The screen output of genbox should >>have indicated how many waters were added - does this number match what you see in the .top? Presumably the first three SOL entries are crystal waters? I >>don't know that pre-existing waters should cause any problem, but it's possible. The difference in the number of atoms is 1016, or 254 TIP4P molecules. <br><br>Before updating to 4.5.4, I removed the crystal waters from the pdb file and now the grompp went fine. The problem was probably the different water notations after the genbox step. Here follows an exemple:<br><br>Crystal water before (original pdb):<br>...<br>HETATM 3999 O HOH A 410 24.263 -7.517 -15.541 1.00
27.99 O <br>HETATM 4000 O HOH A 411 5.682
7.359 2.277 1.00 35.66 O <br>HETATM 4001 O HOH A 412 20.924 0.175 -18.311 1.00 30.25 O <br>HETATM 4002 O HOH A 413 7.366 3.959 -6.173 1.00 36.77 O <br>HETATM 4003 O HOH A 414 0.563 16.043 -5.418 1.00 29.62 O <br>...<br>and the added tip4p waters:<br>...<br> 121SOL OW 1760 0.519 0.692 0.680<br>
121SOL HW1 1761 0.504 0.612 0.731<br>
121SOL HW2 1762 0.601 0.727 0.714<br>
121SOL MW 1763 0.527 0.684 0.692<br>
122SOL OW 1764 0.856 1.378 1.365<br>...<br><br>I just wonder if the romoval of these crystal water may introduce artifacts to the simulation.<br><br>Thanks for your insights!<br><br><br>>>Coincidentally, 59 + 97 + 98 = 254. It looks like genbox wrote the wrong number of molecules it added. If this is the case, please file an issue on >>redmine.gromacs.org with the exact steps taken to reproduce the problem so it can be fixed.<br>>><br>>>-Justin<br>><br>> Thanks for your time.<br>> <br>> Ricardo.<br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
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