求助：用amber做动力学，遇到Error：Could not find angle parameter: os - ca - ha

liuliuliu666

各位老师好，我用amber跑动力学遇到问题，Could not find angle parameter: os - ca - ha，我已经加载了guff立场，还用parmchk2检查缺失参数，生成补充参数文件frcmd
以下是我用的脚本，做到最下面这一步开始出错

module load apps/amber/AmberTools20/hpcx-2.4.1-gcc-7.3.1

source /public/software/apps/amber/amber20_src/amber.sh  

antechamber -i lig.mol2 -fi mol2 -o lig.prepi -fo prepi -c bcc -rn LIG -pf y

parmchk2 -i lig.prepi -f prepi -o lig.frcmod

pdb4amber -i com-noh.pdb -o com.pdb --reduce

tleap

source leaprc.protein.ff14SB

source leaprc.gaff

source leaprc.water.tip3p

loadamberprep lig.prepi

loadamberparams lig.frcmod

set default PBRadii mbondi2

lig=loadpdb sqm.pdb

com = loadpdb com.pdb

receptor=loadpdb receptor.pdb

saveamberparm lig lig.prmtop lig.inpcrd

附件里是我的相关文件，希望大家不吝赐教，特别谢谢大家

abdoman

简单说，小分子的参数不对

sqm.pdb 与com.pdb 里面的小分子各个原子的名字对应吗？

rpestana94

Why you are loading the ligand as pdb and creating the the prepi and frcmod from a mol2 file, it can have different names, try loading the ligand as mol2 file, and should be the same one that you use to create the prepi file

liuliuliu666

abdoman 发表于 2023-12-18 17:22
简单说，小分子的参数不对

sqm.pdb 与com.pdb 里面的小分子各个原子的名字对应吗？

谢谢，确实是小分子的问题，小分子的结构在MOE中查看没问题，但在pdb文件中被分成了三段。

liuliuliu666

rpestana94 发表于 2023-12-18 21:39
Why you are loading the ligand as pdb and creating the the prepi and frcmod from a mol2 file, it can ...

Thank you, I have solved the problem.