24小时热门版块排行榜

>论坛更新日志 (2180)
>虫友互识 (228)
>硕博家园 (81)
>论文投稿 (45)
>博后之家 (43)
>考博 (39)
>教师之家 (37)
>导师招生 (31)
>文献求助 (29)
>论文道贺祈福 (26)
>基金申请 (25)
>休闲灌水 (25)
>考研 (17)
>找工作 (16)
>公派出国 (16)
>第一性原理 (11)

返回列表

当前只显示满足指定条件的回帖，点击这里查看本话题的所有回帖

Jfreda

铁虫 (小有名气)

应助: 0 (幼儿园)
金币: 21.8
帖子: 91
在线: 31.5小时
虫号: 870275

[交流] 【求助】grompp出错

grompp -f em.mdp -c tempwater.gro -p GLP-1R-Boc5_apo.top -o kor-em.tpr

Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
-------------------------------------------------------
Program grompp, VERSION 4.5.1
Source code file: toppush.c, line: 629
Fatal error:
Unknown atomtype HW
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
其中HW是水分子中的氢。

这是我的top文件
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include POPC chain topology
#include "popc.itp"
; Include ligand topology
#include "Boc5.itp"
; Include water topology
#include "./gromos53a6_lipid.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct    fcx       fcy       fcz
1 1    1000    1000    1000
#endif
; Include topology for ions
#include "./gromos53a6_lipid.ff/ions.itp"
[ system ]
; Name
Title card required
[ molecules ]
; Compound       #mols
Protein_chain_A    1
UNK                1
SOL          75128
POP             383

spc.itp文件
[ moleculetype ]
; molname    nrexcl
SOL          2
[ atoms ]
; nr type  resnr residue  atom cgnr    charge    mass
#ifndef HEAVY_H
   1    OW    1 SOL    OW    1    -0.82 15.99940
   2    H    1 SOL HW1    1    0.41 1.00800
   3    H    1 SOL HW2    1    0.41 1.00800
#else
   1    OW    1 SOL    OW    1    -0.82 9.95140
   2    H    1 SOL HW1    1    0.41 4.03200
   3    H    1 SOL HW2    1    0.41 4.03200

gro文件
  328SOL HW152696 6.933 8.639 6.114
  328SOL HW252697 6.801 8.579 6.188
  329SOL    OW52698 7.655 9.446 6.221
  329SOL HW152699 7.636 9.363 6.273
  329SOL HW252700 7.572 9.475 6.173
  330SOL    OW52701 8.839 9.744 6.410
  330SOL HW152702 8.779 9.773 6.335
  330SOL HW252703 8.790 9.677 6.467
  331SOL    OW52704 8.925  11.871 6.960
  331SOL HW152705 8.936  11.845 7.056
  331SOL HW252706 8.827  11.871 6.937
  332SOL    OW52707  12.195 8.268 6.612
  332SOL HW152708  12.122 8.215 6.569
  332SOL HW252709  12.260 8.298 6.541
  333SOL    OW52710  12.310 6.909  11.525
  333SOL HW152711  12.295 6.981  11.458
  333SOL HW252712  12.369 6.838  11.486
  334SOL    OW52713  10.377  10.855  12.640
  334SOL HW152714  10.365  10.953  12.652
  334SOL HW252715  10.412  10.837  12.548
  335SOL    OW52716 9.895  11.732 6.991
  335SOL HW152717 9.896  11.735 7.091
  335SOL HW252718 9.802  11.745 6.959
  336SOL    OW52719 0.569 1.275 1.165
  336SOL HW152720 0.476 1.268 1.128
  336SOL HW252721 0.580 1.364 1.209
  337SOL    OW52722 1.555 1.511 0.703
  337SOL HW152723 1.498 1.495 0.784
  337SOL HW252724 1.496 1.521 0.623
  338SOL    OW52725 1.743 0.618 0.856
  338SOL HW152726 1.776 0.712 0.856
  338SOL HW252727 1.794 0.564 0.922
  339SOL    OW52728 1.135 0.703 0.717
  339SOL HW152729 1.192 0.781 0.692
  339SOL HW252730 1.075 0.729 0.793
  340SOL    OW52731 1.755 0.607 0.231
  340SOL HW152732 1.743 0.594 0.132
  340SOL HW252733 1.725 0.526 0.280
  341SOL    OW52734 0.768 1.144 1.023
  341SOL HW152735 0.690 1.161 1.083
  341SOL HW252736 0.802 1.231 0.987
  342SOL    OW52737 0.850 0.798 1.823
  342SOL HW152738 0.846 0.874 1.888
  342SOL HW252739 0.872 0.834 1.732
  343SOL    OW52740 0.685 1.012 0.665
  343SOL HW152741 0.754 0.996 0.735
力场用的是gromos53a6,我自己看了很久也不知道哪里出错了，哪位高手帮忙指点一下，都卡在那边动不了了。

回复此楼