<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 12"><meta name="Originator" content="Microsoft Word 12"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5Cinter%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_filelist.xml"><link rel="themeData" href="file:///C:%5CDOCUME%7E1%5Cinter%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_themedata.thmx"><link rel="colorSchemeMapping" href="file:///C:%5CDOCUME%7E1%5Cinter%5CLOCALS%7E1%5CTemp%5Cmsohtmlclip1%5C01%5Cclip_colorschememapping.xml"><style>
<!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;
mso-font-charset:1;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;
mso-font-charset:0;
mso-generic-font-family:swiss;
mso-font-pitch:variable;
mso-font-signature:-1610611985 1073750139 0 0 159 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-unhide:no;
mso-style-qformat:yes;
mso-style-parent:"";
margin-top:0in;
margin-right:0in;
margin-bottom:10.0pt;
margin-left:0in;
line-height:115%;
mso-pagination:widow-orphan;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-ascii-font-family:Calibri;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"Times New Roman";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Calibri;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:Arial;
mso-bidi-theme-font:minor-bidi;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-unhide:no;
mso-style-locked:yes;
mso-style-link:"HTML Preformatted";
mso-ansi-font-size:10.0pt;
mso-bidi-font-size:10.0pt;
font-family:"Courier New";
mso-ascii-font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";
mso-hansi-font-family:"Courier New";
mso-bidi-font-family:"Courier New";}
.MsoChpDefault
{mso-style-type:export-only;
mso-default-props:yes;
mso-ascii-font-family:Calibri;
mso-ascii-theme-font:minor-latin;
mso-fareast-font-family:"Times New Roman";
mso-fareast-theme-font:minor-fareast;
mso-hansi-font-family:Calibri;
mso-hansi-theme-font:minor-latin;
mso-bidi-font-family:Arial;
mso-bidi-theme-font:minor-bidi;}
.MsoPapDefault
{mso-style-type:export-only;
margin-bottom:10.0pt;
line-height:115%;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;
mso-header-margin:.5in;
mso-footer-margin:.5in;
mso-paper-source:0;}
div.Section1
{page:Section1;}
-->
</style>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Courier New";">Hi,</span></p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><span style="font-size: 10pt; font-family: "Courier New";"> </span></p>
<pre>I have a problem with grompp.</pre><pre>I want to simulate membrane protein. I adjust the [ molecules ] section to list the number and type of my components</pre><pre>I run grompp and it shows 56 warning about all of atom types in ffG53a6nb.itp (56 atom types are in ffG53a6).</pre>
<pre> </pre><pre>I run pdb2gmx for protein only. Why does it give me these warning?</pre><pre> </pre><pre>I paste warning here:</pre><pre> </pre><pre>Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp</pre>
<pre>Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp</pre><pre>Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp</pre><pre> </pre><pre>WARNING 1 [file ffG53a6nb.itp, line 3]:</pre>
<pre><span style=""> </span>Overriding atomtype O</pre><pre> </pre><pre> </pre><pre>WARNING 2 [file ffG53a6nb.itp, line 4]:</pre><pre><span style=""> </span>Overriding atomtype OM</pre><pre> </pre><pre> </pre><pre>WARNING 3 [file ffG53a6nb.itp, line 5]:</pre>
<pre><span style=""> </span>Overriding atomtype OA</pre><pre> </pre><pre> </pre><pre>WARNING 4 [file ffG53a6nb.itp, line 6]:</pre><pre><span style=""> </span>Overriding atomtype OE</pre><pre> </pre><pre> </pre><pre>WARNING 5 [file ffG53a6nb.itp, line 7]:</pre>
<pre><span style=""> </span>Overriding atomtype OW</pre><pre> </pre><pre> </pre><pre>WARNING 6 [file ffG53a6nb.itp, line 8]:</pre><pre><span style=""> </span>Overriding atomtype N</pre><pre> </pre><pre> </pre><pre>WARNING 7 [file ffG53a6nb.itp, line 9]:</pre>
<pre><span style=""> </span>Overriding atomtype NT</pre><pre> </pre><pre> </pre><pre>WARNING 8 [file ffG53a6nb.itp, line 10]:</pre><pre><span style=""> </span>Overriding atomtype NL</pre><pre> </pre><pre> </pre><pre>WARNING 9 [file ffG53a6nb.itp, line 11]:</pre>
<pre><span style=""> </span>Overriding atomtype NR</pre><pre> </pre><pre> </pre><pre>WARNING 10 [file ffG53a6nb.itp, line 12]:</pre><pre><span style=""> </span>Overriding atomtype NZ</pre><pre> </pre><pre> </pre><pre>WARNING 11 [file ffG53a6nb.itp, line 13]:</pre>
<pre><span style=""> </span>Overriding atomtype NE</pre><pre> </pre><pre> </pre><pre>WARNING 12 [file ffG53a6nb.itp, line 14]:</pre><pre><span style=""> </span>Overriding atomtype C</pre><pre> </pre><pre> </pre><pre>WARNING 13 [file ffG53a6nb.itp, line 15]:</pre>
<pre><span style=""> </span>Overriding atomtype CH0</pre><pre> </pre><pre> </pre><pre>WARNING 14 [file ffG53a6nb.itp, line 16]:</pre><pre><span style=""> </span>Overriding atomtype CH1</pre><pre> </pre><pre> </pre><pre>
WARNING 15 [file ffG53a6nb.itp, line 17]:</pre><pre><span style=""> </span>Overriding atomtype CH2</pre><pre> </pre><pre> </pre><pre>WARNING 16 [file ffG53a6nb.itp, line 18]:</pre><pre><span style=""> </span>Overriding atomtype CH3</pre>
<pre> </pre><pre> </pre><pre>WARNING 17 [file ffG53a6nb.itp, line 19]:</pre><pre><span style=""> </span>Overriding atomtype CH4</pre><pre> </pre><pre> </pre><pre>WARNING 18 [file ffG53a6nb.itp, line 20]:</pre><pre><span style=""> </span>Overriding atomtype CH2r</pre>
<pre> </pre><pre> </pre><pre>WARNING 19 [file ffG53a6nb.itp, line 21]:</pre><pre><span style=""> </span>Overriding atomtype CR1</pre><pre> </pre><pre> </pre><pre>WARNING 20 [file ffG53a6nb.itp, line 22]:</pre><pre><span style=""> </span>Overriding atomtype HC</pre>
<pre> </pre><pre> </pre><pre>WARNING 21 [file ffG53a6nb.itp, line 23]:</pre><pre><span style=""> </span>Overriding atomtype H</pre><pre> </pre><pre> </pre><pre>WARNING 22 [file ffG53a6nb.itp, line 24]:</pre><pre><span style=""> </span>Overriding atomtype DUM</pre>
<pre> </pre><pre> </pre><pre>WARNING 23 [file ffG53a6nb.itp, line 25]:</pre><pre><span style=""> </span>Overriding atomtype S</pre><pre> </pre><pre> </pre><pre>WARNING 24 [file ffG53a6nb.itp, line 26]:</pre><pre><span style=""> </span>Overriding atomtype CU1+</pre>
<pre> </pre><pre> </pre><pre>WARNING 25 [file ffG53a6nb.itp, line 27]:</pre><pre><span style=""> </span>Overriding atomtype CU2+</pre><pre> </pre><pre> </pre><pre>WARNING 26 [file ffG53a6nb.itp, line 28]:</pre><pre><span style=""> </span>Overriding atomtype FE</pre>
<pre> </pre><pre> </pre><pre>WARNING 27 [file ffG53a6nb.itp, line 29]:</pre><pre><span style=""> </span>Overriding atomtype ZN2+</pre><pre> </pre><pre> </pre><pre>WARNING 28 [file ffG53a6nb.itp, line 30]:</pre><pre><span style=""> </span>Overriding atomtype MG2+</pre>
<pre> </pre><pre> </pre><pre>WARNING 29 [file ffG53a6nb.itp, line 31]:</pre><pre><span style=""> </span>Overriding atomtype CA2+</pre><pre> </pre><pre> </pre><pre>WARNING 30 [file ffG53a6nb.itp, line 32]:</pre><pre><span style=""> </span>Overriding atomtype P</pre>
<pre> </pre><pre> </pre><pre>WARNING 31 [file ffG53a6nb.itp, line 33]:</pre><pre><span style=""> </span>Overriding atomtype AR</pre><pre> </pre><pre> </pre><pre>WARNING 32 [file ffG53a6nb.itp, line 34]:</pre><pre><span style=""> </span>Overriding atomtype F</pre>
<pre> </pre><pre> </pre><pre>WARNING 33 [file ffG53a6nb.itp, line 35]:</pre><pre><span style=""> </span>Overriding atomtype CL</pre><pre> </pre><pre> </pre><pre>WARNING 34 [file ffG53a6nb.itp, line 36]:</pre><pre><span style=""> </span>Overriding atomtype BR</pre>
<pre> </pre><pre> </pre><pre>WARNING 35 [file ffG53a6nb.itp, line 37]:</pre><pre><span style=""> </span>Overriding atomtype CMet</pre><pre> </pre><pre> </pre><pre>WARNING 36 [file ffG53a6nb.itp, line 38]:</pre><pre><span style=""> </span>Overriding atomtype OMet</pre>
<pre> </pre><pre> </pre><pre>WARNING 37 [file ffG53a6nb.itp, line 39]:</pre><pre><span style=""> </span>Overriding atomtype NA+</pre><pre> </pre><pre> </pre><pre>WARNING 38 [file ffG53a6nb.itp, line 40]:</pre><pre><span style=""> </span>Overriding atomtype CL-</pre>
<pre> </pre><pre> </pre><pre>WARNING 39 [file ffG53a6nb.itp, line 41]:</pre><pre><span style=""> </span>Overriding atomtype CChl</pre><pre> </pre><pre> </pre><pre>WARNING 40 [file ffG53a6nb.itp, line 42]:</pre><pre><span style=""> </span>Overriding atomtype CLChl</pre>
<pre> </pre><pre> </pre><pre>WARNING 41 [file ffG53a6nb.itp, line 43]:</pre><pre><span style=""> </span>Overriding atomtype HChl</pre><pre> </pre><pre> </pre><pre>WARNING 42 [file ffG53a6nb.itp, line 44]:</pre><pre><span style=""> </span>Overriding atomtype SDmso</pre>
<pre> </pre><pre> </pre><pre>WARNING 43 [file ffG53a6nb.itp, line 45]:</pre><pre><span style=""> </span>Overriding atomtype CDmso</pre><pre> </pre><pre> </pre><pre>WARNING 44 [file ffG53a6nb.itp, line 46]:</pre><pre><span style=""> </span>Overriding atomtype ODmso</pre>
<pre> </pre><pre> </pre><pre>WARNING 45 [file ffG53a6nb.itp, line 47]:</pre><pre><span style=""> </span>Overriding atomtype CCl4</pre><pre> </pre><pre> </pre><pre>WARNING 46 [file ffG53a6nb.itp, line 48]:</pre><pre><span style=""> </span>Overriding atomtype CLCl4</pre>
<pre> </pre><pre> </pre><pre>WARNING 47 [file ffG53a6nb.itp, line 49]:</pre><pre><span style=""> </span>Overriding atomtype FTFE</pre><pre> </pre><pre> </pre><pre>WARNING 48 [file ffG53a6nb.itp, line 50]:</pre><pre><span style=""> </span>Overriding atomtype CTFE</pre>
<pre> </pre><pre> </pre><pre>WARNING 49 [file ffG53a6nb.itp, line 51]:</pre><pre><span style=""> </span>Overriding atomtype CHTFE</pre><pre> </pre><pre> </pre><pre>WARNING 50 [file ffG53a6nb.itp, line 52]:</pre><pre><span style=""> </span>Overriding atomtype OTFE</pre>
<pre> </pre><pre> </pre><pre>WARNING 51 [file ffG53a6nb.itp, line 53]:</pre><pre><span style=""> </span>Overriding atomtype CUrea</pre><pre> </pre><pre> </pre><pre>WARNING 52 [file ffG53a6nb.itp, line 54]:</pre><pre><span style=""> </span>Overriding atomtype OUrea</pre>
<pre> </pre><pre> </pre><pre>WARNING 53 [file ffG53a6nb.itp, line 55]:</pre><pre><span style=""> </span>Overriding atomtype NUrea</pre><pre> </pre><pre> </pre><pre>WARNING 54 [file ffG53a6nb.itp, line 56]:</pre><pre><span style=""> </span>Overriding atomtype SI</pre>
<pre> </pre><pre> </pre><pre>WARNING 55 [file ffG53a6nb.itp, line 57]:</pre><pre><span style=""> </span>Overriding atomtype MNH3</pre><pre> </pre><pre> </pre><pre>WARNING 56 [file ffG53a6nb.itp, line 58]:</pre><pre><span style=""> </span>Overriding atomtype MW</pre>
<pre> </pre><pre>Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp</pre><pre>Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp</pre><pre>Generated 825 of the 2346 non-bonded parameter combinations</pre>
<pre>Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp</pre><pre>Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp</pre><pre>Excluding 3 bonded neighbours molecule type 'protein'</pre>
<pre>turning all bonds into constraints...</pre><pre>Excluding 3 bonded neighbours molecule type 'DOPC'</pre><pre>turning all bonds into constraints...</pre><pre>Excluding 2 bonded neighbours molecule type 'SOL'</pre>
<pre>turning all bonds into constraints...</pre><pre>Excluding 1 bonded neighbours molecule type 'NA+'</pre><pre>turning all bonds into constraints...</pre><pre>Excluding 1 bonded neighbours molecule type 'CL-'</pre>
<pre>turning all bonds into constraints...</pre><pre>processing coordinates...</pre><pre>double-checking input for internal consistency...</pre><pre>Reading position restraint coords from nvt-mutated_bi.gro</pre><pre>renumbering atomtypes...</pre>
<pre>converting bonded parameters...</pre><pre>initialising group options...</pre><pre>processing index file...</pre><pre>Making dummy/rest group for Acceleration containing 18916 elements</pre><pre>Making dummy/rest group for Freeze containing 18916 elements</pre>
<pre>Making dummy/rest group for Energy Mon. containing 18916 elements</pre><pre>Number of degrees of freedom in T-Coupling group Protein is 724.85</pre><pre>Number of degrees of freedom in T-Coupling group DOPC is 13622.15</pre>
<pre>Number of degrees of freedom in T-Coupling group SOL_NA+_CL- is 23613.00</pre><pre>Making dummy/rest group for User1 containing 18916 elements</pre><pre>Making dummy/rest group for User2 containing 18916 elements</pre>
<pre>Making dummy/rest group for XTC containing 18916 elements</pre><pre>Making dummy/rest group for Or. Res. Fit containing 18916 elements</pre><pre>Making dummy/rest group for QMMM containing 18916 elements</pre><pre>T-Coupling<span style=""> </span>has 3 element(s): Protein DOPC SOL_NA+_CL-</pre>
<pre>Energy Mon.<span style=""> </span>has 1 element(s): rest</pre><pre>Acceleration<span style=""> </span>has 1 element(s): rest</pre><pre>Freeze<span style=""> </span>has 1 element(s): rest</pre><pre>
User1<span style=""> </span>has 1 element(s): rest</pre><pre>User2<span style=""> </span>has 1 element(s): rest</pre><pre>VCM<span style=""> </span>has 2 element(s): Protein_DOPC SOL_NA+_CL-</pre>
<pre>XTC<span style=""> </span>has 1 element(s): rest</pre><pre>Or. Res. Fit<span style=""> </span>has 1 element(s): rest</pre><pre>QMMM<span style=""> </span>has 1 element(s): rest</pre><pre>
Checking consistency between energy and charge groups...</pre><pre>Calculating fourier grid dimensions for X Y Z</pre><pre>Using a fourier grid of 48x45x48, spacing 0.152 0.160 0.154</pre><pre>Estimate for the relative computational load of the PME mesh part: 0.35</pre>
<pre>This run will generate roughly 3 Mb of data</pre><pre>writing run input file...</pre><pre> </pre><pre>There were 56 warnings</pre><pre> </pre><pre>-------------------------------------------------------</pre><pre>Program grompp, VERSION 4.0.5</pre>
<pre>Source code file: gmx_fatal.c, line: 481</pre><pre> </pre><pre>Fatal error:</pre><pre>Too many warnings (56), grompp terminated.</pre>
<div style="border-style: none none solid; border-color: -moz-use-text-color -moz-use-text-color windowtext; border-width: medium medium 1pt; padding: 0in 0in 1pt;"><pre style="border: medium none ; padding: 0in;">If you are sure all warnings are harmless, use the -maxwarn option.</pre>
</div>
<pre> </pre><br clear="all"><br>thanks in advance,<br>Afsaneh <br>